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 |
|---|---|---|---|---|---|
=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>.
=head1 NAME
Bio::EnsEMBL::Compara::RunnableDB::AncestralAllelesForIndels::RunAncestralAllelesComplete
=head1 SYNOPSIS
This RunnableDB module is part of the AncestralAllelesForIndels pipeline.
=head1 DESCRIPTION
This RunnableDB module creates and analyses the consequences of an indel event for each base in an alignment. It writes the 'event' to a file which can used with the Variant Effect Predictor.
=cut
package Bio::EnsEMBL::Compara::RunnableDB::AncestralAllelesForIndels::RunAncestralAllelesComplete;
use strict;
use warnings;
use base ('Bio::EnsEMBL::Compara::RunnableDB::AncestralAllelesForIndels::AncestralAllelesCompleteBase');
use Bio::EnsEMBL::DBSQL::DBAdaptor;
sub fetch_input {
my $self = shift;
}
sub run {
my $self = shift;
$self->run_cmd();
}
sub write_output {
my $self = shift @_;
my $output = $self->param('output');
my $sql = "INSERT INTO statistics (seq_region, seq_region_start, seq_region_end, total_bases, all_N, low_complexity, multiple_gats, no_gat, insufficient_gat, long_alignment, align_all_N, num_bases_analysed) VALUES (?,?,?,?,?,?,?,?,?,?,?,?)";
my $sth = $self->compara_dba->dbc->prepare($sql);
$sth->execute($output->{'seq_region'}, $output->{'seq_region_start'}, $output->{'seq_region_end'}, $output->{'total_bases'}, $output->{'all_N'},$output->{'count_low_complexity'}, $output->{'multiple_gats'},$output->{'no_gat'},$output->{'insufficient_gat'},$output->{'long_alignment'},$output->{'align_all_N'},$output->{'num_bases_analysed'});
my $statistics_id = $self->dbc->db_handle->last_insert_id(undef, undef, 'statistics', 'statistics_id');
$sth->finish;
$sql = "INSERT INTO event (statistics_id, indel, type, detail, detail1, improvement, detail2, count) VALUES (?,?,?,?,?,?,?,?)";
$sth = $self->compara_dba->dbc->prepare($sql);
foreach my $event (keys %{$output->{'sum_types'}}) {
my $count = $output->{'sum_types'}{$event};
my ($indel, $type, $detail, $detail1, $improve, $detail2) = $event =~ /(insertion|deletion)_(novel|recovery|unsure)_(of_allele_base|strict|shuffle|realign|neighbouring_deletion|neighbouring_insertion|complex)_{0,1}(strict1|shuffle1){0,1}_{0,1}(better|worse){0,1}_{0,1}(polymorphic_insertion|polymorphic_deletion|complex_polymorphic_insertion|complex_polymorphic_deletion|funny_polymorphic_insertion|funny_polymorphic_deletion){0,1}/;
$sth->execute($statistics_id, $indel, $type, $detail, $detail1, $improve, $detail2, $count);
}
$sth->finish;
};
#
# Run ortheus and parse the output
#
sub run_ortheus {
my ($self, $compara_dba, $dump_dir, $ordered_fasta_files, $ordered_fasta_headers, $ga_lookup, $tree_string, $mlss, $ref_ga, $flank, $curr_pos, $verbose) = @_;
#Call ortheus
my $fasta_str = join " ", @{$ordered_fasta_files};
my $ortheus_exe = $self->param('ortheus_bin');
my $tree_state_file = $dump_dir . "/output.$$.tree";
my $out_align = $dump_dir . "/output.$$.mfa";
my $out_score = $dump_dir . "/output.$$.score";
my $nuc_freq = "0.3 0.2 0.2 0.3";
#my $ortheus_cmd = "$ortheus_exe -b '$tree_string' -c $align_fasta -a $fasta_str -u $tree_state_file -s 0 -j 0 -d $out_align -n $nuc_freq -x $out_score";
my $ortheus_cmd = "$ortheus_exe -b '$tree_string' -a $fasta_str -u $tree_state_file -s 0 -j 0 -d $out_align -n $nuc_freq -x $out_score";
my @output = `$ortheus_cmd 2>&1`;
#Capture error messages
#print "output=$output[0]\n";
if (0 == $?) {
#print "OK\n";
} else {
open ERR, "/tmp/kb3_ortheus_error_file" || die "Unable to open /tmp/kb3_ortheus_error_file";
while (<ERR>) {
print "ERR $_";
}
close ERR;
print "Failed $!\n";
$self->warning("ortheus execution failed at position $curr_pos\n$ortheus_cmd\n");
return;
}
my ($new_tree, $new_score) = $self->parse_results($compara_dba, $dump_dir, $ga_lookup, $ordered_fasta_files, $tree_string, $ordered_fasta_headers, $verbose);
$new_tree = $self->finalise_tree($compara_dba, $new_tree, $mlss, $ref_ga);
if ($verbose) {
foreach my $genomic_align_node (@{$new_tree->get_all_sorted_genomic_align_nodes()}) {
foreach my $genomic_align (@{$genomic_align_node->genomic_align_group->get_all_GenomicAligns}) {
my $name;
if ($genomic_align->dnafrag_id == -1) {
$name = "Ancestral";
next;
} else {
$name = $genomic_align->genome_db->name;
}
if ($flank && $ref_ga && ($name eq $ref_ga->genome_db->name &&
$genomic_align->dnafrag_id == $ref_ga->dnafrag_id &&
$genomic_align->dnafrag_start == $ref_ga->dnafrag_start &&
$genomic_align->dnafrag_end == $ref_ga->dnafrag_end)) {
my $highlight = $self->get_highlighter($genomic_align, $flank);
print OUT "$highlight\n";
}
print OUT $genomic_align->aligned_sequence . " " . $name . " " . $genomic_align->dnafrag_id . " " . $genomic_align->dnafrag_start . " " . $genomic_align->dnafrag_end . " " .$genomic_align->cigar_line . "\n" if ($verbose);
}
}
}
$self->tidy_up_files($dump_dir);
return ($new_tree, $new_score);
}
1;
| danstaines/ensembl-compara | modules/Bio/EnsEMBL/Compara/RunnableDB/AncestralAllelesForIndels/RunAncestralAllelesComplete.pm | Perl | apache-2.0 | 6,404 |
#
# Copyright 2018 Centreon (http://www.centreon.com/)
#
# Centreon is a full-fledged industry-strength solution that meets
# the needs in IT infrastructure and application monitoring for
# service performance.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
#
package os::windows::wsman::mode::listservices;
use base qw(centreon::plugins::mode);
use strict;
use warnings;
sub new {
my ($class, %options) = @_;
my $self = $class->SUPER::new(package => __PACKAGE__, %options);
bless $self, $class;
$self->{version} = '1.0';
$options{options}->add_options(arguments =>
{
"name:s" => { name => 'name' },
"regexp" => { name => 'use_regexp' },
});
return $self;
}
sub check_options {
my ($self, %options) = @_;
$self->SUPER::init(%options);
}
sub manage_selection {
my ($self, %options) = @_;
$self->{result} = $self->{wsman}->request(uri => 'http://schemas.microsoft.com/wbem/wsman/1/wmi/root/cimv2/*',
wql_filter => 'Select Name, DisplayName, StartMode, State From Win32_Service',
result_type => 'hash',
hash_key => 'Name');
foreach my $name (sort(keys %{$self->{result}})) {
# Get all without a name
next if (!defined($self->{option_results}->{name}));
next if (!defined($self->{option_results}->{use_regexp}) && $name eq $self->{option_results}->{name});
next if (defined($self->{option_results}->{use_regexp}) && $name =~ /$self->{option_results}->{name}/);
$self->{output}->output_add(long_msg => "Skipping service '" . $name . "': no matching filter name");
delete $self->{result}->{$name};
}
}
sub run {
my ($self, %options) = @_;
# $options{wsman} = wsman object
$self->{wsman} = $options{wsman};
$self->manage_selection();
foreach my $name (sort(keys %{$self->{result}})) {
$self->{output}->output_add(long_msg => "'" . $name . "' [DisplayName = " . $self->{output}->to_utf8($self->{result}->{$name}->{DisplayName}) . '] [' .
'StartMode = ' . $self->{result}->{$name}->{StartMode} . '] [' .
'State = ' . $self->{result}->{$name}->{State} .
']');
}
$self->{output}->output_add(severity => 'OK',
short_msg => 'List services:');
$self->{output}->display(nolabel => 1, force_ignore_perfdata => 1, force_long_output => 1);
$self->{output}->exit();
}
sub disco_format {
my ($self, %options) = @_;
$self->{output}->add_disco_format(elements => ['name', 'display_name', 'start_mode', 'state']);
}
sub disco_show {
my ($self, %options) = @_;
# $options{wsman} = wsman object
$self->{wsman} = $options{wsman};
$self->manage_selection();
foreach my $name (sort(keys %{$self->{result}})) {
$self->{output}->add_disco_entry(name => $name,
display_name => $self->{output}->to_utf8($self->{result}->{$name}->{DisplayName}),
start_mode => $self->{result}->{$name}->{StartMode},
state => $self->{result}->{$name}->{State}
);
}
}
1;
__END__
=head1 MODE
List Windows Services.
=over 8
=item B<--name>
Set the service name.
=item B<--regexp>
Allows to use regexp to filter service name (with option --name).
=back
=cut | wilfriedcomte/centreon-plugins | os/windows/wsman/mode/listservices.pm | Perl | apache-2.0 | 4,272 |
#
# Output.pm
# Created by: Adam Jacob, Marchex, <adam@marchex.com>
# Created on: 10/31/2006 12:58:58 PM PST
#
# $Id: $
#
# Author:: Adam Jacob (<adam@opscode.com>)
# Copyright:: Copyright (c) 2008 Adam Jacob
# License:: Apache License, Version 2.0
#
# 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 Sid::Format::Output;
use strict;
use warnings;
use Moose;
use Params::Validate qw(:all);
with 'Sid::Role::Log4perl';
has 'store_output' => ( is => 'rw', isa => 'Bool', default => 0 );
has 'saved_output' => ( is => 'rw', isa => 'Str', );
has 'search_fields' => ( is => 'rw', isa => 'ArrayRef' );
has 'search_data' => ( is => 'rw', isa => 'ArrayRef', required => 1 );
sub BUILD {
my ($self, $params) = @_;
if (! exists($params->{'search_fields'})) {
my %search_fields;
foreach my $sr (@{$params->{'search_data'}}) {
foreach my $key (keys(%{$sr->{'fields'}})) {
$search_fields{$key} = 1 unless exists($search_fields{$key});
}
}
my @temp = sort(keys(%search_fields));
$self->search_fields(\@temp);
}
}
sub output {
my $self = shift;
my $outputstring = shift;
if ($self->store_output) {
my $co = $self->saved_output;
if (defined($co)) {
$self->saved_output($co . $outputstring . "\n");
} else {
$self->saved_output($outputstring . "\n");
}
} else {
$self->log->info($outputstring);
}
}
1;
| adamhjk/sid | lib/Sid/Format/Output.pm | Perl | apache-2.0 | 1,980 |
package RPi::PIGPIO::Assistant;
=head1 NAME
RPi::PIGPIO::Assistant - Methods for reverse engeniering devices
=head1 DESCRIPTION
This module is a helper that can be used to easely debug things on a GPIO
=head1 SYNOPSIS
You can use this one-liner to monitor level changes on a gpio
perl -Ilib -MRPi::PIGPIO::Assistant -e "RPi::PIGPIO::Assistant->new('192.168.1.23')->intercept(gpio => 18);"
Note: This example assumes that pigpiod is running on the Raspberry Pi with the IP address 192.168.1.23
=cut
use strict;
use warnings;
use RPi::PIGPIO ':all';
=head1 METHODS
=head2 new
Creates a new RPi::PIGPIO::Assistant object
Params:
=over 4
=item 1. ip address of the Raspi running the pigpiod daemon
=item 2. port on which pigpiod is listening (defaults to 8888)
=back
or
=over 4
=item 1. an instance of a C<RPi::PIGPIO>
=back
=cut
sub new {
my ($class, $param1, $param2) = @_;
my $self = {};
if (ref($param1) eq "RPi::PIGPIO") {
$self->{pi} = $param1;
}
else {
$self->{pi} = RPi::PIGPIO->connect($param1, $param2);
}
bless $self, $class;
}
=head2 intercept
Monitors a given GPIO for level changes
Params:
=over 4
=item gpio => GPIO which you want to monitor (mandatory)
=item pud => Pull-up/down level to set for the given gpio, (optional) one of
=over 8
=item 0 => OFF
=item 1 => DOWN
=item 2 => UP
=back
=back
Usage:
$assistant->intercept(gpio => 18, pud => 0);
=cut
sub intercept {
my ($self, %params) = @_;
local $|=1;
my $sock = IO::Socket::INET->new(
PeerAddr => $self->{pi}{host},
PeerPort => $self->{pi}{port},
Proto => 'tcp'
);
my $gpio = $params{gpio};
die "Assistant failed to connect to $self->{pi}{host}:$self->{pi}{port}!" unless $sock;
my $handle = $self->{pi}->send_command_on_socket($sock, PI_CMD_NOIB, 0, 0);
my $lastLevel = $self->{pi}->send_command(PI_CMD_BR1, 0, 0);
#Subscribe to level changes on the DHT22 GPIO
$self->{pi}->send_command(PI_CMD_NB, $handle , 1 << $gpio);
$self->{pi}->set_mode($gpio,PI_INPUT);
if (defined $params{pud}) {
$self->{pi}->set_pull_up_down($gpio, $params{pud});
}
my $MSG_SIZE = 12;
while (1) {
my $buffer;
my $read_buf;
$sock->recv($buffer, $MSG_SIZE);
while ( length($buffer) < $MSG_SIZE ) {
$sock->recv($read_buf, $MSG_SIZE-length($buffer));
$buffer .= $read_buf;
}
my ($seq, $flags, $tick, $level) = unpack('SSII', $buffer);
if ($flags && NTFY_FLAGS_WDOG) {
print "Watchdog signal received: timeout in GPIO : ".($flags & NTFY_FLAGS_GPIO)."\n";
}
else {
my $changed = $level ^ $lastLevel;
$lastLevel = $level;
if ( (1<<$gpio) & $changed ) {
my $newLevel = 0;
if ( (1<<$gpio) & $level ) {
$newLevel = 1;
}
print "Received : seq => $seq | flags => $flags | tick => $tick | level => $newLevel \n";
}
}
}
}
1; | gliganh/RPi-PIGPIO | lib/RPi/PIGPIO/Assistant.pm | Perl | apache-2.0 | 3,337 |
#
# Copyright 2021 Centreon (http://www.centreon.com/)
#
# Centreon is a full-fledged industry-strength solution that meets
# the needs in IT infrastructure and application monitoring for
# service performance.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
#
package hardware::devices::eltek::enexus::snmp::plugin;
use strict;
use warnings;
use base qw(centreon::plugins::script_snmp);
sub new {
my ($class, %options) = @_;
my $self = $class->SUPER::new(package => __PACKAGE__, %options);
bless $self, $class;
$self->{version} = '0.1';
%{$self->{modes}} = (
'alarms' => 'hardware::devices::eltek::enexus::snmp::mode::alarms',
'battery' => 'hardware::devices::eltek::enexus::snmp::mode::battery',
'load' => 'hardware::devices::eltek::enexus::snmp::mode::load',
'outputs' => 'hardware::devices::eltek::enexus::snmp::mode::outputs'
);
return $self;
}
1;
__END__
=head1 PLUGIN DESCRIPTION
Check Eltek eNexus in SNMP (SmartPack2 V2.x, SmartPack S V2.x and Compack V2.x).
=cut
| Tpo76/centreon-plugins | hardware/devices/eltek/enexus/snmp/plugin.pm | Perl | apache-2.0 | 1,549 |
#
# Copyright 2021 Centreon (http://www.centreon.com/)
#
# Centreon is a full-fledged industry-strength solution that meets
# the needs in IT infrastructure and application monitoring for
# service performance.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
#
package storage::ibm::storwize::ssh::mode::components::enclosure;
use strict;
use warnings;
sub load {
my ($self) = @_;
$self->{ssh_commands} .= 'echo "==========lsenclosure=========="; lsenclosure -delim : ; echo "===============";';
}
sub check {
my ($self) = @_;
$self->{output}->output_add(long_msg => "Checking enclosures");
$self->{components}->{enclosure} = {name => 'enclosures', total => 0, skip => 0};
return if ($self->check_filter(section => 'enclosure'));
return if ($self->{results} !~ /==========lsenclosure==.*?\n(.*?)==============/msi);
my $content = $1;
my $result = $self->{custom}->get_hasharray(content => $content, delim => ':');
foreach (@$result) {
next if ($self->check_filter(section => 'enclosure', instance => $_->{id}));
$self->{components}->{enclosure}->{total}++;
$self->{output}->output_add(
long_msg => sprintf(
"enclosure '%s' status is '%s' [instance: %s].",
$_->{id},
$_->{status},
$_->{id}
)
);
my $exit = $self->get_severity(label => 'default', section => 'enclosure', value => $_->{status});
if (!$self->{output}->is_status(value => $exit, compare => 'ok', litteral => 1)) {
$self->{output}->output_add(
severity => $exit,
short_msg => sprintf(
"Enclosure '%s' status is '%s'",
$_->{id},
$_->{status}
)
);
}
}
}
1;
| Tpo76/centreon-plugins | storage/ibm/storwize/ssh/mode/components/enclosure.pm | Perl | apache-2.0 | 2,345 |
# Copyright 2001-2006 The Apache Software Foundation
#
# 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 AxKit2::Transformer::XPathScript;
use strict;
use warnings;
use AxKit2::Constants;
use XML::XPathScript;
use AxKit2::Utils qw(bytelength);
use base qw(AxKit2::Transformer);
sub new {
my $class = shift;
my $stylesheet = shift;
my $output_style = shift;
return bless { stylesheet => $stylesheet,
output_style => $output_style }, $class;
}
sub transform {
my $self = shift;
my ($pos, $processor) = @_;
$self->log( LOGDEBUG, 'in transform' );
my $dom = $processor->dom;
my $xps = XML::XPathScript->new( stylesheetfile => $self->{stylesheet} );
my $parser = XML::LibXML->new;
my $result = $xps->transform( $dom );
my $out_dom;
unless ( eval { $out_dom = $parser->parse_string( $result ) } ) {
$out_dom = $parser->parse_string(
'<xpathscript:wrapper '
.'xmlns:xpathscript="http://babyl.dyndns.org/xpathscript" '
.'xpathscript:type="cdata">'
.'<![CDATA['
. $result
. ']]></xpathscript:wrapper>' );
}
return $out_dom, sub { $self->output(@_) };
}
sub output {
my ($self, $client, $dom) = @_;
$self->log( LOGDEBUG, 'in output' );
my $out;
my $ct = 'text/xml';
if ( my( $root ) = eval { $dom->findnodes( '/xpathscript:wrapper' ) } ) {
warn "xpathscript:wrapper";
$ct = $root->getAttribute( 'type' )
if $root->getAttribute( 'type' );
if ( $ct eq 'cdata' ) {
$ct = 'text/plain';
$out = $root->textContent;
}
else {
$out .= $_->toString for $root->childNodes;
}
}
else {
warn "pure XML, baby";
$out = $dom->toStringHTML;
}
# XPathScript_OutputStyle trumps all
$ct = $self->{output_style} if $self->{output_style};
$client->headers_out->header('Content-Length', bytelength($out));
$client->headers_out->header( 'Content-Type' => $ct );
$client->send_http_headers;
$client->write($out);
}
1;
| gitpan/AxKit2 | lib/AxKit2/Transformer/XPathScript.pm | Perl | apache-2.0 | 2,653 |
package ISC::BIND::Stats::UI::View::JSON;
use strict;
use base 'Catalyst::View::JSON';
=head1 NAME
ISC::BIND::Stats::UI::View::JSON - Catalyst JSON View
=head1 SYNOPSIS
See L<ISC::BIND::Stats::UI>
=head1 DESCRIPTION
Catalyst JSON View.
=head1 AUTHOR
Francisco Obispo
=head1 LICENSE
This library is free software, you can redistribute it and/or modify
it under the same terms as Perl itself.
=cut
1;
| isc-projects/bind9-stats | ISC-BIND-Stats-UI/lib/ISC/BIND/Stats/UI/View/JSON.pm | Perl | bsd-2-clause | 412 |
#!/usr/bin/perl
use warnings;
use strict;
#use Devel::Size qw(total_size);
# Load and parse header
my $header=<>;
chomp $header;
my $c=0;
my %headers=();
foreach my $h (split('\t', $header))
{
$headers{$h} = $c;
$c++;
}
my %data=();
while(my $l=<>)
{
chomp $l;
my @line=split('\t',$l);
foreach my $h (keys %headers)
{
$data{$line[$headers{USER_ID}]}{$h} = $line[$headers{$h}];
}
}
#print total_size(\%data) . "\n";
| petricek/datatools | bin/load-user-data.pl | Perl | bsd-2-clause | 428 |
%% geom.pl
%%
%% contains basic computational geometry predicates.
%%
%% Copyright (C) 2003 DG Lane
%% depends on vector
:- consult(vector).
:- consult(coord_sys).
%% mesh_volume/2
%%
%% predicate to unify /3 with the element-wise vector addition
%% of the input vectors.
mesh_volume(Mesh, Volume) :-
%% use center of mesh bounds as origin
mesh_bounds(Mesh, [Xmin, Ymin, Zmin], [Xmax, Ymax, Zmax]),
Xo is (Xmax - Xmin) / 2.0,
Yo is (Ymax - Ymin) / 2.0,
Zo is (Zmax - Zmin) / 2.0,
%% compute individual facet signed volumes, based on origin
findall(Volume_Facet,
(
%% for each mesh,
member(Facet, Mesh),
%% compute volume
facet_volume(Facet, [Xo, Yo, Zo], Volume_Facet)
),
%% accumulate in Volumes
Volumes),
%% sum the resulting list of volumes
sumlist(Volumes, Volume).
facet_volume([V1, V2, V3], Orig, Volume) :-
Volume is_v ((V1 - Orig) x (V2 - Orig)) * (V3 - Orig) / 6.0.
%% mesh_volume/2
%%
%% predicate to unify /3 with the element-wise vector addition
%% of the input vectors.
mesh_bounds(Mesh, [Xmin, Ymin, Zmin], [Xmax, Ymax, Zmax]) :-
%% accumulate all vertices (flatten mesh)
findall(Vert,
( member(Facet, Mesh),
member(Vert, Facet)
),
Verts),
%% transpose to create list of Xs, Ys, and Zs
transpose(Verts, [Xs, Ys, Zs]),
%% form min and max of lists
min(Xs, Xmin), max(Xs, Xmax),
min(Ys, Ymin), max(Ys, Ymax),
min(Zs, Zmin), max(Zs, Zmax).
%% dist_line_mesh/3
%%
%% predicate to unify /3 with minimum distance from Mesh to Line
dist_line_mesh(Line, Mesh, Distance) :-
%% accumulate all distances to line
findall(VertDist,
( member(Facet, Mesh),
member(Vertex, Facet),
dist_point_line(Vertex, Line, VertDist)
),
Distances),
%% return min distance
min(Distances, Distance).
ray_mesh_intersect([Orig, Dir], Mesh, P) :-
findall([IntersectPoint, Dist],
(
member(Facet, Mesh),
ray_facet_intersect([Orig, Dir], Facet, IntersectPoint),
vec_diff(Orig, IntersectPoint, Offset),
vec_length(Offset, Dist)
),
IntersectionPairs),
transpose(IntersectionPairs, [_, Distances]),
min(Distances, D),
member([P, D], IntersectionPairs).
%% point_on_mesh/3
%%
%% predicate to unify /3 with the element-wise vector addition
%% of the input vectors.
point_on_mesh(Point, Mesh, Epsilon) :-
dist_point_mesh(Point, Mesh, Distance),
is_approx_equal(Distance, 0, Epsilon).
%% dist_point_mesh/3
%%
%% predicate to unify /3 with the element-wise vector addition
%% of the input vectors.
dist_point_mesh(Point, Mesh, Distance) :-
%% accumulate all distances
findall(FacetDist,
( member(Facet, Mesh),
dist_point_facet(Point, Facet, FacetDist)
),
Distances),
%% determine minimum
min(Distances, Distance).
ray_facet_intersect([Orig, Dir], [F1, F2, F3], P) :-
%% compute barycentric coordinates for the origin point,
%% along the direction vector
bary_coord_facet(Orig, [F1, F2, F3], Dir, [S, T, U]),
%% do we intersect the triangle?
S >= 0,
T >= 0,
S + T =< 1,
%% make sure we are in the correct hemispace
U =< 0,
%% compute the offset to the intersection point
P is_v F1 + S * (F2 - F1) + T * (F3 - F1).
%% dist_point_facet/3
%%
%% predicate to unify /3 with the element-wise vector addition
%% of the input vectors.
dist_point_facet(Point, Verts, Distance) :-
bary_coord_facet(Point, Verts, _, [S, T, U]),
S >= 0,
T >= 0,
S + T =< 1, !,
Distance is abs(U).
dist_point_facet(Point, [V1, V2, V3], Distance) :-
dist_point_seg(Point, [V1, V2], Dist1_2),
dist_point_seg(Point, [V2, V3], Dist2_3),
dist_point_seg(Point, [V3, V1], Dist3_1),
min([Dist1_2, Dist2_3, Dist3_1], Distance).
facet_plane([V1, V2, V3], [V1, Dir]) :-
Dir is_v vec_norm((V2 - V1) x (V3 - V1)).
%% bary_coord_facet/3
%%
%% predicate to unify /3 with the element-wise vector addition
%% of the input vectors.
bary_coord_facet(Point, [F1, F2, F3], N, [S, T, Z]) :-
%% use F1 as origin
W is_v Point - F1,
U is_v F2 - F1,
V is_v F3 - F1,
(
%% do we need to compute the normal?
var(N),
%% form cross product of two legs of triangle
N is_v U x V, !;
%% otherwise, leave N alone
true ),
%% use perp-dot function to form S and T
proj_perp(W, U, V, N, S),
proj_perp(W, V, U, N, T),
%% use unit normal vector to determine Z
Z is_v W * vec_norm(N).
proj_perp(P, U, V, N, Proj) :-
Cross is_v V x N,
Cross_U is_v Cross * U, Cross_U =\= 0.0,
Proj is_v Cross * P / Cross_U.
%% poly_area/2
%%
%% predicate to unify /3 with the element-wise vector addition
%% of the input vectors.
poly_area(Polygon, Plane, Area) :-
%% accumulate all individual edge areas in to Areas list
findall(Area_Edge,
( nth0(N, Polygon, Vert1),
nth1(N, Polygon, Vert2),
edge_area([Vert1, Vert2], Plane, Area_Edge)
),
Areas),
%% sum Areas list
sumlist(Areas, Area).
edge_area([U, V], [Orig, Normal], Area) :-
Area is_v ((U - Orig) x (V - Orig)) * Normal / 2.0.
%% dist_point_poly/3
%%
%% minimum distance from a point to a polygon
dist_point_poly(Point, Poly, Distance) :-
findall(Dist,
( member(V1, Poly),
nextto(V1, V2, Poly),
dist_point_seg(Point, [V1, V2], Dist)),
DistAll),
min(DistAll, Distance).
%% planes_with_polys/3
%%
%% a list of polygons is associated with planes for each polygon
planes_with_polys([Poly1 | Polys_t], Normal,
[[[Orig1, Normal], Poly1] | PlanesWithPolys_t]) :-
poly_plane(Poly1, [Orig1, Normal], _),
planes_with_polys(Polys_t, Normal, PlanesWithPolys_t).
planes_with_polys([[] | Polys_t], Normal, PlanesWithPolys_t) :-
planes_with_polys(Polys_t, Normal, PlanesWithPolys_t).
planes_with_polys([], _, []).
%% poly_plane/3
%%
%% associates a polygon with a plane containing the polygon.
poly_plane(Poly, [V1, Plane_normal], _) :-
%% if the normal is provided
nonvar(Plane_normal),
%% just choose one of the members of the polygon as the plane point
member(V1, Poly), !.
poly_plane(Poly, [V1, Plane_normal], MinCross) :-
%% choose three points
nth0(N1, Poly, V1),
nth0(N2, Poly, V2), N2 > N1,
nth0(N3, Poly, V3), N3 > N2,
%% form cross product
Cross is_v (V2 - V1) x (V3 - V1),
%% check that length > MinCross
L is_v vec_len(Cross), L > MinCross, !,
%% normalize cross product to form plane normal
Plane_normal is_v vec_norm(Cross) ;
%% if failed on length check, try smaller min crossing
SmallerMinCross is MinCross * 0.5,
%% recursive call
poly_plane(Poly, [V1, Plane_normal], SmallerMinCross).
%% orient_polys/2
%% orient_poly/2
%%
%% associates a list of unoriented polys w/ planes with a list of
%% oriented polys w/ planes
orient_polys(PlanesWithPolys, PlanesWithOrientedPolys) :-
%% form the list for all members
findall([Plane, OrientedPoly],
%% remove the currently selected poly from the list
( select([Plane, Poly], PlanesWithPolys,
RemPlanesWithPolys),
%% orient the currently selected
orient_poly([Plane, Poly], RemPlanesWithPolys,
OrientedPoly)
),
%% collect into oriented list
PlanesWithOrientedPolys).
orient_poly([[PlaneOrigin, PlaneNormal], Poly],
OtherPlanesWithPolys, OrientedPoly) :-
%% locate another polygon in the list
member([OtherPlane, OtherPoly], OtherPlanesWithPolys),
%% on the same plane as this one
planes_approx_equal([PlaneOrigin, PlaneNormal], OtherPlane, 1e-6),
format('Other Plane = ~p ~n', [OtherPlane]),
%% pick a point on this polygon
nth0(0, Poly, Vert),
%% if it is inside the other polygon,
point_inside_poly(OtherPoly, PlaneNormal, Vert),
%% compute the signed area of the polygon
poly_area(Poly, [PlaneOrigin, PlaneNormal], PolyArea),
(
%% then the area should be negative
PolyArea < 0.0,
%% so orientation is OK
OrientedPoly = Poly, ! ;
%% otherwise, reverse orientation
reverse(Poly, OrientedPoly), !).
orient_poly([Plane, Poly], _, OrientedPoly) :-
%% compute the signed area of the polygon
poly_area(Poly, Plane, PolyArea),
(
%% area should be positive
PolyArea > 0.0,
%% so orientation is OK
OrientedPoly = Poly, ! ;
%% otherwise, reverse orientation
reverse(Poly, OrientedPoly)).
%% point_inside_poly/3
%%
%% test that a point is inside a polygon -- point and polygon must be coplanar
point_inside_poly(Poly, PlaneNormal, Point) :-
%% form the direction vector for the intersection
member(Axis, [[1, 0, 0], [0, 1, 0], [1, 0, 0]]),
Dir is_v PlaneNormal x Axis,
Dir_length is_v vec_len(Dir), Dir_length > 0.1, !,
%% locate all intersections for the polygon
findall(IntersectPoint,
( nth1(N, Poly, V1),
nth0(N, Poly, V2),
ray_seg_intersect([Point, Dir], PlaneNormal,
[V1, V2], IntersectPoint)
),
IntersectPoints),
%% locate all duplicates within the list
findall(DuplicateIntersection,
( nth0(M, IntersectPoints, DuplicateIntersection),
nth0(N, IntersectPoints, OtherIntersection),
N > M,
dist_point_point(DuplicateIntersection,
OtherIntersection, Dist),
is_approx_equal(Dist, 0, 1e-6)
),
DuplicateIntersections),
%% count the number of intersections minus duplicates
length(IntersectPoints, IntersectCount),
length(DuplicateIntersections, DuplicateCount),
%% if odd, then the point is inside the polygon
1 =:= (IntersectCount - DuplicateCount) mod 2.
%% ray_seg_intersect/4
%%
%% determines intersection of ray with a segment, if it exists.
%% ray and segment must be coplanar
ray_seg_intersect([Orig, Dir], PlaneNormal, [S1, S2], P) :-
%% form the normal to the ray
Normal is_v Dir x PlaneNormal,
Normal_length is_v vec_len(Normal),
is_approx_equal(Normal_length, 1.0, 1e-6),
%% form the offset from segment end to start, dot normal
Denom is_v (S2 - S1) * Normal,
%% denom must be sufficiently non-zero
abs(Denom) > 1e-6,
%% form scalar for intersection
Lambda is_v (Orig - S1) * Normal / Denom,
%% scalar must be >= 0.0 and =< 1.0 for intersection to
%% lie on segment
Lambda >= 0.0, Lambda =< 1.0,
%% form scalar product of S1 + Lambda * Ds (intersection point)
P is_v Lambda * (S2 - S1) + S1,
%% check that intersection is on the ray
DirSign is_v (P - Orig) * Dir,
DirSign >= 0.0.
%% dist_point_seg/4
%%
%% predicate to unify /3 with the element-wise vector addition
%% of the input vectors.
dist_point_seg(Point, [Seg1, Seg2], Distance) :-
%% use Seg1 as origin
Offset is_v Seg2 - Seg1,
Point_offset is_v Point - Seg1,
%% Scale is scalar of projection
Scale is_v (Point_offset * Offset) / (Offset * Offset),
%% test for range of scale
(
%% Scale =< 0.0 -> point is closest to Seg1
Scale =< 0.0, !,
Distance is_v vec_len(Point_offset) ;
%% Scale >= 1.0 -> point is closest to Seg2
Scale >= 1.0, !,
Distance is_v vec_len(Point - Seg2) ;
%% otherwise point is closest to its projection on to the segment
Distance is_v vec_len(Point_offset - Scale * Offset)
).
%% planes_approx_equal/3
%%
%% test that two planes are approximately eqivalent
planes_approx_equal([O1, N1], [O2, N2], Epsilon) :-
%% use O1 as origin
Offset is_v O2 - O1,
%% Test Offset <dot> N1 ~= 0
Dot1 is_v Offset * N1,
is_approx_equal(Dot1, 0, Epsilon),
%% Test Offset <dot> N2 ~= 0
Dot2 is_v Offset * N2,
is_approx_equal(Dot2, 0, Epsilon).
%% point_on_plane/3
%%
%% determines if the point lies on the plane, up to the specified epsilon
point_on_plane(Point, Plane, Epsilon) :-
dist_point_plane(Point, Plane, Distance),
is_approx_equal(Distance, 0, Epsilon).
%% dist_point_plane/4
%%
%% predicate to unify /3 with the distance from the point to the
%% plane.
dist_point_plane(Point, [PlanePoint, PlaneNorm], Distance) :-
Point_offset is_v Point - PlanePoint,
Point_proj is_v vec_proj(Point_offset, vec_norm(PlaneNorm)),
Distance is_v vec_len(Point_proj).
%% point_on_line/3
%%
%% asserts that the point lies on the line, to within a distance
%% of Epsilon.
point_on_line(Point, Line, Epsilon) :-
dist_point_line(Point, Line, Distance),
is_approx_equal(Distance, 0, Epsilon).
%% dist_point_line/4
%%
%% predicate to unify /3 with the element-wise vector addition
%% of the input vectors.
dist_point_line(Point, [LinePoint, LineDir], Distance) :-
Point_offset is_v Point - LinePoint,
Point_proj is_v vec_proj(Point_offset, vec_norm(LineDir)),
dist_point_point(Point_offset, Point_proj, Distance).
%% dist_point_point/3
%%
%% predicate to unify /3 with the element-wise vector addition
%% of the input vectors.
dist_point_point(PtL, PtR, Distance) :-
Distance is_v vec_len(PtL - PtR).
| dg1an3/ALGT | algt_tests/pl/geom_op.pl | Perl | bsd-2-clause | 12,574 |
#!/usr/bin/env perl
use Mojolicious::Lite;
use Mojo::ByteStream 'b';
use Mojo::Date;
use Mojo::JSON qw/true false encode_json decode_json/;
use strict;
use warnings;
use Mojo::JWT;
use Mojo::File qw/path/;
use Mojo::Util qw/slugify/;
# This is an API fake server with fixtures
my $secret = 's3cr3t';
my $fixture_path = path(Mojo::File->new(__FILE__)->dirname)->child('..', 'fixtures');
our %tokens = (
'access_token' => "4dcf8784ccfd26fac9bdb82778fe60e2",
'refresh_token' => "hlWci75xb8atDiq3924NUSvOdtAh7Nlf9z",
'access_token_2' => "abcde",
'access_token_3' => 'jvgjbvjgzucgdwuiKHJK',
'refresh_token_2' => "fghijk",
'new_client_id' => 'fCBbQkA2NDA3MzM1Yw==',
'new_client_secret' => 'KUMaFxs6R1WGud4HM22w3HbmYKHMnNHIiLJ2ihaWtB4N5JxGzZgyqs5GTLutrORj',
'auth_token_1' => 'mscajfdghnjdfshtkjcuynxahgz5il'
);
helper get_token => sub {
my ($c, $token) = @_;
return $tokens{$token}
};
# Legacy:
helper jwt_encode => sub {
shift;
return Mojo::JWT->new(
secret => $secret,
token_type => 'api_token',
expires => time + (3 * 34 * 60 * 60),
claims => { @_ }
);
};
# Legacy;
helper jwt_decode => sub {
my ($c, $auth) = @_;
$auth =~ s/\s*api_token\s+//;
return Mojo::JWT->new(secret => $secret)->decode($auth);
};
# Expiration helper
helper expired => sub {
my ($c, $auth, $set) = @_;
$auth =~ s/^[^ ]+? //;
if ($set) {
$c->app->log->debug("Set $auth for expiration");
$c->app->defaults('auth_' . $auth => 1);
return 1;
};
$c->app->log->debug("Check $auth for expiration: " . (
$c->app->defaults('auth_' . $auth) // '0'
));
return $c->app->defaults('auth_' . $auth);
};
# Load fixture responses
helper 'load_response' => sub {
my $c = shift;
my $q_name = shift;
my $file = $fixture_path->child("response_$q_name.json");
$c->app->log->debug("Load response from $file");
unless (-f $file) {
return {
status => 500,
json => {
errors => [[0, 'Unable to load query response from ' . $file]]
}
}
};
my $response = $file->slurp;
my $decode = decode_json($response);
unless ($decode) {
return {
status => 500,
json => {
errors => [[0, 'Unable to parse JSON']]
}
}
};
return $decode;
};
app->defaults('oauth.client_list' => []);
# Base page
get '/v1.0/' => sub {
shift->render(text => 'Fake server available');
};
get '/v1.0/redirect-target-a' => sub {
shift->render(text => 'Redirect Target!');
} => 'redirect-target';
# Base page
get '/v1.0/redirect' => sub {
my $c = shift;
$c->res->code(308);
$c->res->headers->location($c->url_for('redirect-target')->to_abs);
return $c->render(text => '');
};
# Search fixtures
get '/v1.0/search' => sub {
my $c = shift;
my $v = $c->validation;
$v->optional('q');
$v->optional('page');
$v->optional('ql');
$v->optional('cq');
$v->optional('count');
$v->optional('context');
$v->optional('offset');
$v->optional('pipes');
$v->optional('cutoff')->in(qw/true false/);
$c->app->log->debug('Receive request');
# Response q=x&ql=cosmas3
if ($v->param('ql') && $v->param('ql') eq 'cosmas3') {
return $c->render(
status => 400,
json => {
"\@context" => "http://korap.ids-mannheim.de/ns/koral/0.3/context.jsonld",
"errors" => [[307,"cosmas3 is not a supported query language!"]]
});
};
if (!$v->param('q')) {
return $c->render(%{$c->load_response('query_no_query')});
};
if ($v->param('q') eq 'error') {
return $c->render(
status => 500,
inline => '<html><head>ERROR</head></html>'
);
};
my @slug_base = ($v->param('q'));
push @slug_base, 'o' . $v->param('offset') if defined $v->param('offset');
push @slug_base, 'c' . $v->param('count') if defined $v->param('count');
push @slug_base, 'co' . $v->param('cutoff') if defined $v->param('cutoff');
push @slug_base, 'cq' if defined $v->param('cq');
push @slug_base, 'p' . $v->param('pipes') if defined $v->param('pipes');
# Get response based on query parameter
my $response = $c->load_response('query_' . slugify(join('_', @slug_base)));
# Check authentification
if (my $auth = $c->req->headers->header('Authorization')) {
$c->app->log->debug("There is an authorization header $auth");
my $jwt;
if ($auth =~ /^Bearer/) {
# Username unknown in OAuth2
$response->{json}->{meta}->{authorized} = 'yes';
}
elsif ($auth =~ /^api_token/ && ($jwt = $c->jwt_decode($auth))) {
$response->{json}->{meta}->{authorized} = $jwt->{username} if $jwt->{username};
};
# Code is expired
if ($c->expired($auth)) {
$c->app->log->debug("The access token has expired");
return $c->render(
status => 401,
json => {
errors => [[2003, 'Access token is expired']]
}
);
}
# Auth token is invalid
if ($auth =~ /^Bearer inv4lid/) {
$c->app->log->debug("The access token is invalid");
return $c->render(
status => 401,
json => {
errors => [[2011, 'Access token is invalid']]
}
);
}
};
if ($v->param('pipes')) {
$response->{json}->{meta}->{pipes} = $v->param('pipes');
};
# Set page parameter
if ($v->param('page')) {
$response->{json}->{meta}->{startIndex} = $v->param("startIndex");
};
# Simple search fixture
$c->render(%$response);
$c->app->log->debug('Rendered result');
return 1;
};
# Textinfo fixtures
get '/v1.0/corpus/:corpusId/:docId/:textId' => sub {
my $c = shift;
my $file = join('_', (
'textinfo',
$c->stash('corpusId'),
$c->stash('docId'),
$c->stash('textId')
));
my $slug = slugify($file);
# Get response based on query parameter
my $response = $c->load_response($slug);
return $c->render(%$response);
};
# Matchinfo fixtures
get '/v1.0/corpus/:corpusId/:docId/:textId/:matchId/matchInfo' => sub {
my $c = shift;
my $file = join('_', (
'matchinfo',
$c->stash('corpusId'),
$c->stash('docId'),
$c->stash('textId'),
$c->stash('matchId')
));
my $slug = slugify($file);
# Get response based on query parameter
my $response = $c->load_response($slug);
return $c->render(%$response);
};
# Statistics endpoint
get '/v1.0/statistics' => sub {
my $c = shift;
my $v = $c->validation;
$v->optional('cq');
my @list = 'corpusinfo';
if ($v->param('cq')) {
push @list, $v->param('cq');
};
my $slug = slugify(join('_', @list));
# Get response based on query parameter
my $response = $c->load_response($slug);
return $c->render(%$response);
};
############
# Auth API #
############
# Request API token
get '/v1.0/auth/logout' => sub {
my $c = shift;
if (my $auth = $c->req->headers->header('Authorization')) {
if ($auth =~ /^Bearer/) {
$c->app->log->debug('Server-Logout: ' . $auth);
return $c->render(json => { msg => [[0, 'Fine!']]});
}
elsif (my $jwt = $c->jwt_decode($auth)) {
my $user = $jwt->{username} if $jwt->{username};
$c->app->log->debug('Server-Logout: ' . $user);
return $c->render(json => { msg => [[0, 'Fine!']]});
};
};
return $c->render(status => 400, json => { error => [[0, 'No!']]});
};
# Request API token
get '/v1.0/auth/apiToken' => sub {
my $c = shift;
# Get auth header
my $auth = $c->req->headers->authorization;
# Authorization missing or not basic
if (!$auth || $auth !~ s/\s*Basic\s+//gi) {
return $c->render(
json => {
error => [[2, 'x']]
}
);
};
# Decode header
my ($username, $pwd) = @{b($auth)->b64_decode->split(':')->to_array};
# the password is 'pass'
if ($pwd) {
# the password is 'pass'
if ($pwd eq 'pass') {
# Render info with token
my $jwt = $c->jwt_encode(username => $username);
# Render in the Kustvakt fashion:
return $c->render(
format => 'html',
text => encode_json({
%{$jwt->claims},
expires => $jwt->expires,
token => $jwt->encode,
token_type => 'api_token'
})
);
}
elsif ($pwd eq 'ldaperr') {
return $c->render(
format => 'html',
status => 401,
json => {
"errors" => [[2022,"LDAP Authentication failed due to unknown user or password!"]]
}
);
};
return $c->render(
json => {
error => [[2004, undef]]
}
);
};
return $c->render(
json => {
error => [[2004, undef]]
}
);
};
# Request API token
post '/v1.0/oauth2/token' => sub {
my $c = shift;
my $grant_type = $c->param('grant_type') // 'undefined';
if ($grant_type eq 'password') {
# Check for wrong client id
if ($c->param('client_id') ne '2') {
return $c->render(
json => {
"error_description" => "Unknown client with " . $_->{client_id},
"error" => "invalid_client"
},
status => 401
);
}
# Check for wrong client secret
elsif ($c->param('client_secret') ne 'k414m4r-s3cr3t') {
return $c->render(
json => {
"error_description" => "Invalid client credentials",
"error" => "invalid_client"
},
status => 401
);
}
# Check for wrong user name
elsif ($c->param('username') !~ /^t.st$/) {
return $c->render(json => {
error => [[2004, undef]]
});
}
# Check for ldap error
elsif ($c->param('password') eq 'ldaperr') {
return $c->render(
format => 'html',
status => 401,
json => {
"errors" => [
[
2022,
"LDAP Authentication failed due to unknown user or password!"
]
]
}
);
}
# Check for wrong password
elsif ($c->param('password') ne 'pass') {
return $c->render(json => {
format => 'html',
status => 401,
"errors" => [[2022,"LDAP Authentication failed due to unknown user or password!"]]
});
}
# Return fine access
return $c->render(
json => {
"access_token" => $c->get_token('access_token'),
"refresh_token" => $c->get_token('refresh_token'),
"scope" => "all",
"token_type" => "Bearer",
"expires_in" => 86400
});
}
# Refresh token
elsif ($grant_type eq 'refresh_token') {
if ($c->param('refresh_token') eq 'inv4lid') {
return $c->render(
status => 400,
json => {
"error_description" => "Refresh token is expired",
"error" => "invalid_grant"
}
);
};
$c->app->log->debug("Refresh the token in the mock server!");
return $c->render(
status => 200,
json => {
"access_token" => $c->get_token("access_token_2"),
"refresh_token" => $c->get_token("refresh_token_2"),
"token_type" => "Bearer",
"expires_in" => 86400
}
);
}
# Get auth_token_1
elsif ($grant_type eq 'authorization_code') {
if ($c->param('code') eq $tokens{auth_token_1}) {
return $c->render(
status => 200,
json => {
"access_token" => $tokens{access_token_3},
"expires_in" => 31536000,
"scope" => 'match_info search openid',
"token_type" => "Bearer"
}
);
};
}
# Unknown token grant
else {
return $c->render(
status => 400,
json => {
"errors" => [
[
0, "Grant Type unknown", $grant_type
]
]
}
)
}
};
# Revoke API token
post '/v1.0/oauth2/revoke' => sub {
my $c = shift;
my $refresh_token = $c->param('token');
if ($c->param('client_secret') ne 'k414m4r-s3cr3t') {
return $c->render(
json => {
"error_description" => "Invalid client credentials",
"error" => "invalid_client"
},
status => 401
);
};
return $c->render(
text => ''
)
};
# Register a client
post '/v1.0/oauth2/client/register' => sub {
my $c = shift;
my $json = $c->req->json;
if ($json->{redirectURI}) {
return $c->render(
status => 400,
json => {
errors => [
[
201,
"Unrecognized field \"redirectURI\" (class de.ids_mannheim.korap.web.input.OAuth2ClientJson), not marked as ignorable (5 known properties: \"redirect_uri\", \"type\", \"name\", \"description\", \"url\"])\n at [Source: (org.eclipse.jetty.server.HttpInputOverHTTP); line: 1, column: 94] (through reference chain: de.ids_mannheim.korap.web.input.OAuth2ClientJson[\"redirectURI\"])"
]
]
}
);
};
my $name = $json->{name};
my $desc = $json->{description};
my $type = $json->{type};
my $url = $json->{url};
my $redirect_url = $json->{redirect_uri};
my $list = $c->app->defaults('oauth.client_list');
push @$list, {
"client_id" => $tokens{new_client_id},
"client_name" => $name,
"client_description" => $desc,
"client_url" => $url
};
# Confidential server application
if ($type eq 'CONFIDENTIAL') {
return $c->render(json => {
client_id => $tokens{new_client_id},
client_secret => $tokens{new_client_secret}
});
};
# Desktop application
return $c->render(json => {
client_id => $tokens{new_client_id}
});
};
# Register a client
post '/v1.0/oauth2/client/list' => sub {
my $c = shift;
my $v = $c->validation;
$v->required('super_client_id');
$v->required('super_client_secret');
if ($v->has_error) {
return $c->render(
json => [],
status => 400
);
};
# $c->param('client_secret');
# Is empty [] when nothing registered
return $c->render(
json => $c->stash('oauth.client_list'),
status => 200
);
};
# Get token list
post '/v1.0/oauth2/token/list' => sub {
my $c = shift;
return $c->render(json => [
{
"client_description" => "Nur ein Beispiel",
"client_id" => $tokens{new_client_id},
"client_name" => "Beispiel",
"client_url" => "",
"created_date" => "2021-04-14T19:40:26.742+02:00[Europe\/Berlin]",
"expires_in" => "31533851",
"scope" => [
"match_info",
"search",
"openid"
],
"token" => "jhkhkjhk_hjgjsfz67i",
"user_authentication_time" => "2021-04-14T19:39:41.81+02:00[Europe\/Berlin]"
}
]);
};
del '/v1.0/oauth2/client/deregister/:client_id' => sub {
my $c = shift;
my $client_id = $c->stash('client_id');
my $list = $c->app->defaults('oauth.client_list');
my $break = -1;
for (my $i = 0; $i < @$list; $i++) {
if ($list->[$i]->{client_id} eq $client_id) {
$break = $i;
last;
};
};
if ($break != -1) {
splice @$list, $break, 1;
}
else {
return $c->render(
json => {
error_description => "Unknown client with $client_id.",
error => "invalid_client"
},
status => 401
);
};
return $c->render(
json => $c->stash('oauth.client_list'),
status => 200
);
};
post '/v1.0/oauth2/authorize' => sub {
my $c = shift;
my $type = $c->param('response_type');
my $client_id = $c->param('client_id');
my $redirect_uri = $c->param('redirect_uri');
if ($type eq 'code') {
return $c->redirect_to(
Mojo::URL->new($redirect_uri)->query({
code => $tokens{auth_token_1},
scope => 'match_info search openid'
})
);
}
};
#######################
# Query Reference API #
#######################
use CHI;
my $chi = CHI->new(
driver => 'Memory',
global => 1
);
# Store query
put '/v1.0/query/~:user/:query_name' => sub {
my $c = shift;
my $user = $c->stash('user');
my $qname = $c->stash('query_name');
if ($chi->is_valid($qname)) {
return $c->render(
json => {
errors => [
{
message => 'Unable to store query reference'
}
]
}, status => 400
);
};
my $json = $c->req->json;
my $store = {
name => $qname,
koralQuery => { '@type' => 'Okay' },
query => $json->{query},
queryType => $json->{queryType},
type => $json->{type},
queryLanguage => $json->{queryLanguage},
};
if (exists $json->{description}) {
$store->{description} = $json->{description}
};
# Set query reference
$chi->set($qname => $store);
my $queries = $chi->get('~queries') // [];
push @$queries, $qname;
$chi->set('~queries' => $queries);
return $c->render(
status => 201,
text => ''
);
};
# Get query
get '/v1.0/query/~:user/:query_name' => sub {
my $c = shift;
my $user = $c->stash('user');
my $qname = $c->stash('query_name');
my $json = $chi->get($qname);
if ($json) {
return $c->render(
json => $json
);
};
return $c->render(
json => {
errors => [
{
message => 'Query reference not found'
}
]
}, status => 404
);
};
# Get all queries
get '/v1.0/query/~:user' => sub {
my $c = shift;
my $user = $c->stash('user');
my $qs = $chi->get('~queries') // [];
my @queries = ();
foreach (@$qs) {
push @queries, $chi->get($_);
};
return $c->render(json => { refs => \@queries });
};
# Store query
del '/v1.0/query/~:user/:query_name' => sub {
my $c = shift;
my $user = $c->stash('user');
my $qname = $c->stash('query_name');
$chi->remove($qname);
my $queries = $chi->get('~queries') // [];
my @clean = ();
foreach (@$queries) {
push @clean, $_ unless $_ eq $qname
};
$chi->set('~queries' => \@clean);
return $c->render(
status => 200,
text => ''
);
};
post '/v1.0/oauth2/revoke/super' => sub {
my $c = shift;
my $s_client_id = $c->param('super_client_id');
my $s_client_secret = $c->param('super_client_secret');
my $token = $c->param('token');
return $c->render(text => 'SUCCESS');
};
app->start;
__END__
# Temporary:
my $collection_query = {
'@type' => "koral:docGroup",
"operation" => "operation:or",
"operands" => [
{
'@type' => "koral:docGroup",
"operation" => "operation:and",
"operands" => [
{
'@type' => "koral:doc",
"key" => "title",
"match" => "match:eq",
"value" => "Der Birnbaum",
"type" => "type:string"
},
{
'@type' => "koral:doc",
"key" => "pubPlace",
"match" => "match:eq",
"value" => "Mannheim",
"type" => "type:string"
},
{
'@type' => "koral:docGroup",
"operation" => "operation:or",
"operands" => [
{
'@type' => "koral:doc",
"key" => "subTitle",
"match" => "match:eq",
"value" => "Aufzucht oder Pflege",
"type" => "type:string"
},
{
'@type' => "koral:doc",
"key" => "subTitle",
"match" => "match:eq",
"value" => "Gedichte",
"type" => "type:string"
}
]
}
]
},
{
'@type' => "koral:doc",
"key" => "pubDate",
"match" => "match:geq",
"value" => "2015-03-05",
"type" => "type:date"
}
]
};
| KorAP/Kalamar | t/server/mock.pl | Perl | bsd-2-clause | 18,994 |
package PTC::Device;
require 5.000;
use Exporter;
use lib qw(/opt/perl-traffic-control/lib);
use PTC::Utils;
use Carp;
@ISA = qw(Exporter);
@EXPORT = qw(getPreviewMessage updateWLANnetMessage clearWLANnetMessage getWLANnetMessage getWLANnetClientMessage saveClientDevice showHPNAAddress loadHPNAClient checkRegister getHPNAPassword saveHPNAPassword addClient updateClient LANWORLD);
# Needs reason check
sub getWLANnetMessage
{
my $username=shift;
my $sth = $main::dbh_ptc->prepare("SELECT StartTime,ticket FROM blacklist WHERE UserName = '$username' AND StopTime = '0000-00-00 00:00:00' ;");
$sth->execute();
my @row;
my $msg="";
while (@row = $sth->fetchrow_array ) {
$msg{$row[0]}=$row[1];
}
return \%msg;
}
sub getPreviewMessage
{
my $dbh=shift;
my $sth = $dbh->prepare("SELECT StartTime,ticket FROM blacklist WHERE id=1 ;");
$sth->execute();
my @row;
my $msg="";
while (@row = $sth->fetchrow_array ) {
$msg{$row[0]}=$row[1];
}
return \%msg;
}
sub getWLANnetClientMessage
{
my $clientid=shift;
#print "SELECT StartTime,ticket FROM blacklist WHERE clientid = '$clientid' AND active = 1";
my $sth = $main::dbh_ptc->prepare("SELECT StartTime,ticket FROM blacklist WHERE clientid = '$clientid' AND active=1;");
$sth->execute();
my @row;
my %msg=();
while (@row = $sth->fetchrow_array ) {
# print $row[0].$row[1];
$msg{$row[0]}=$row[1];
}
#print time();
return \%msg;
}
sub clearWLANnetMessage
{
my $clientid=shift;
if ($clientid)
{
my $sth = $main::dbh_ptc->do("UPDATE blacklist SET StopTime = NOW(),active=0 WHERE clientid = '$clientid' AND active=1 ;");
}
#$sth->execute();
# my @row;
#my $msg="";
#while ( @row = $sth->fetchrow_array ) {
#$msg=$msg." ".$row[0]
#}
#return $msg;
}
sub updateWLANnetMessage
{
my $clientid=shift;
if ($clientid)
{
my $sth = $main::dbh_ptc->do("UPDATE blacklist SET ReadTime = NOW() WHERE clientid = '$clientid' AND active=1 ;");
}
}
sub loadHPNAClient
{
my $username=shift;
$username=~s/\@wlanmail.com//;
my %hpnaClients;
my $sth = $main::dbh_hpna->prepare("SELECT Username,Attribute,Value FROM radreply WHERE UserName = '$username' ORDER BY Attribute;");
$sth->execute();
my @row;
while ( @row = $sth->fetchrow_array ) {
$hpnaClients{$row[0]}{$row[1]}=$row[2];
}
return \%hpnaClients;
}
sub addClient
{
my ($username,$password,$clientid,$speed)=@_;
if (!defined $speed)
{
$speed="1024/1024";
}
$main::dbh_hpna->do("INSERT INTO radcheck VALUES (NULL,'$username','Cleartext-Password',':=','$password')");
$main::dbh_hpna->do("INSERT INTO radreply VALUES (NULL,'$username','Reply-Message',':=','$clientid/$username')");
$main::dbh_hpna->do("INSERT INTO radreply VALUES (NULL,'$username','clientid',':=','$clientid')");
$main::dbh_hpna->do("INSERT INTO radreply VALUES (NULL,'$username','Filter-Id',':=','$speed')");
my $error_str="Added";
return \$error_str;
}
sub saveClientDevice
{
my ($mac,$filterid,$replymessage)=@_;
$mac=lc($mac);
if ($mac !~m#(..\:..\:..\:..\:..\:..)#)
{
my $error_str="Laitteisto-osoite ei kelpaa : $mac";
return \$error_str;
}
if ($replymessage =~m#^(\d+)\/.*#)
{
$clientid=$1;;
if (&checkRegister($mac))
{
my $error_str="Laitteisto-osoite on jo käytössä / MAC-Address is already registered";
$error_str=$main::dbh_hpna->do("UPDATE radreply set Value='$replymessage' where UserName='$mac' and Attribute='Reply-Message'");
if ($error_str eq "0E0")
{
$main::dbh_hpna->do("INSERT INTO radreply VALUES (NULL,'$mac','Reply-Message',':=','$replymessage')");
$main::dbh_hpna->do("INSERT INTO radreply VALUES (NULL,'$mac','clientid',':=','$clientid')");
}
elsif ($error_str eq 1)
{
}
else
{
$error_str="!REPLY:".$error_str."!";
return \$error_str;
}
if (defined $filterid)
{
$error_str=$main::dbh_hpna->do("UPDATE radreply SET Value='$filterid' where UserName='$mac' and Attribute='Filter-Id'");
if ($error_str eq "0E0")
{
$main::dbh_hpna->do("INSERT INTO radreply VALUES (NULL,'$mac','Filter-Id',':=','$filterid')");
return 1;
}
elsif ($error_str eq 1)
{
return $error_str;
}
else
{
$error_str="!FILTER:".$error_str."!";
return \$error_str;
}
}
$error_str="OK $clientid";
return \$error_str;
return 0;
return \$error_str;
}
else
{
$main::dbh_hpna->do("INSERT INTO radcheck VALUES (NULL,'$mac','Cleartext-Password',':=','getinfo')");
$main::dbh_hpna->do("INSERT INTO radreply VALUES (NULL,'$mac','Reply-Message',':=','$replymessage')");
$main::dbh_hpna->do("INSERT INTO radreply VALUES (NULL,'$mac','clientid',':=','$clientid')");
if (defined $filterid)
{
$main::dbh_hpna->do("INSERT INTO radreply VALUES (NULL,'$mac','Filter-Id',':=','$filterid')");
my $error_str="OK $clientid";
return \$error_str;
return 1;
}
my $error_str="OK $clientid";
return \$error_str;
return 0;
}
}
else
{
my $error_str="Reply-Message not valid";
return \$error_str;
}
my $error_str="OK";
return \$error_str;
}
sub showHPNAAddress
{
my $ref=loadHPNAClient($username);
my %hpnaClients=%$ref;
foreach (keys %hpnaClients)
{
my $ref=$hpnaClients{$_}{'Calling-Station-Id'};
my %temphash=%$ref;
foreach (keys %temphash)
{
Tvalue("Rekisteröity HPNA-MAC",$_);
}
}
}
sub checkRegister
{
my $mac=shift;
my $found=0;
my $sth = $main::dbh_hpna->prepare("SELECT Username,Attribute,Value FROM radcheck WHERE UserName = '$mac' and Attribute='clientid' ORDER BY Attribute;");
$sth->execute();
my @row;
while ( @row = $sth->fetchrow_array ) {
$found++;
}
return $found;
}
return 1;
| mongrelx/perl-traffic-control | lib/PTC/HPNA.pm | Perl | mit | 6,739 |
# <@LICENSE>
# 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.
# </@LICENSE>
=head1 NAME
Mail::SpamAssassin::Bayes - support for learning classifiers
=head1 DESCRIPTION
This is the general class used to train a learning classifier with new samples
of spam and ham mail, and classify based on prior training.
Prior to version 3.3.0, the default Bayes implementation was here; if you're
looking for information on that, it has moved to
C<Mail::SpamAssassin::Plugin::Bayes>.
=cut
package Mail::SpamAssassin::Bayes;
use strict;
use warnings;
# use bytes;
use re 'taint';
use Mail::SpamAssassin;
use Mail::SpamAssassin::PerMsgStatus;
use Mail::SpamAssassin::Logger;
use Mail::SpamAssassin::Util qw(untaint_var);
our @ISA = qw();
###########################################################################
sub new {
my $class = shift;
$class = ref($class) || $class;
my ($main) = @_;
my $self = {
'main' => $main,
'conf' => $main->{conf},
'use_ignores' => 1,
};
bless ($self, $class);
$self->{main}->call_plugins("learner_new");
$self;
}
###########################################################################
sub finish {
my $self = shift;
# we don't need to do the plugin; Mail::SpamAssassin::finish() does
# that for us
%{$self} = ();
}
###########################################################################
# force the Bayes dbs to be closed, if they haven't already been; called
# at the end of scan operation, or when switching between user IDs,
# or when C<Mail::SpamAssassin::finish_learner()> is called.
#
sub force_close {
my $self = shift;
my $quiet = shift;
$self->{main}->call_plugins("learner_close", { quiet => $quiet });
}
###########################################################################
sub ignore_message {
my ($self,$PMS) = @_;
return 0 unless $self->{use_ignores};
my $ig_from = $self->{main}->call_plugins ("check_wb_list",
{ permsgstatus => $PMS, type => 'from', list => 'bayes_ignore_from' });
my $ig_to = $self->{main}->call_plugins ("check_wb_list",
{ permsgstatus => $PMS, type => 'to', list => 'bayes_ignore_to' });
my $ignore = $ig_from || $ig_to;
dbg("bayes: not using bayes, bayes_ignore_from or _to rule") if $ignore;
return $ignore;
}
###########################################################################
sub learn {
my ($self, $isspam, $msg, $id) = @_;
return unless $self->{conf}->{use_learner};
return unless defined $msg;
if( $self->{use_ignores} ) # Remove test when PerMsgStatus available.
{
# DMK, koppel@ece.lsu.edu: Hoping that the ultimate fix to bug 2263 will
# make it unnecessary to construct a PerMsgStatus here.
my $PMS = Mail::SpamAssassin::PerMsgStatus->new($self->{main}, $msg);
my $ignore = $self->ignore_message($PMS);
$PMS->finish();
return 0 if $ignore;
}
return $self->{main}->call_plugins("learn_message", { isspam => $isspam, msg => $msg, id => $id });
}
###########################################################################
sub forget {
my ($self, $msg, $id) = @_;
return unless $self->{conf}->{use_learner};
return unless defined $msg;
return $self->{main}->call_plugins("forget_message", { msg => $msg, id => $id });
}
###########################################################################
sub sync {
my ($self, $sync, $expire, $opts) = @_;
return 0 unless $self->{conf}->{use_learner};
if ($sync) {
$self->{main}->call_plugins("learner_sync", $opts );
}
if ($expire) {
$self->{main}->call_plugins("learner_expire_old_training", $opts );
}
return 0;
}
###########################################################################
sub is_scan_available {
my $self = shift;
return 0 unless $self->{conf}->{use_learner};
return $self->{main}->call_plugins("learner_is_scan_available");
}
###########################################################################
sub dump_bayes_db {
my($self, $magic, $toks, $regex) = @_;
return 0 unless $self->{conf}->{use_learner};
return $self->{main}->call_plugins("learner_dump_database", {
magic => $magic, toks => $toks, regex => $regex });
}
1;
| apache/spamassassin | lib/Mail/SpamAssassin/Bayes.pm | Perl | apache-2.0 | 4,935 |
=head1 LICENSE
Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.
=cut
=pod
=head1 NAME
Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::GenerateSSPict
=head1 DESCRIPTION
This Hive analysis will create secondary structure plots based on the
secondary structures (in bracket notation) created by Infernal.
In addition to secondary structure plots for the whole alignments
of the family, plots for individual members are also created.
=head1 CONTACT
Please email comments or questions to the public Ensembl
developers list at <http://lists.ensembl.org/mailman/listinfo/dev>.
Questions may also be sent to the Ensembl help desk at
<http://www.ensembl.org/Help/Contact>
=head1 APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with an underscore (_)
=cut
package Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::GenerateSSPict;
use strict;
use warnings;
use Data::Dumper;
use base ('Bio::EnsEMBL::Compara::RunnableDB::BaseRunnable');
sub fetch_input {
my ($self) = @_;
my $nc_tree_id = $self->param_required('gene_tree_id');
my $nc_tree = $self->compara_dba->get_GeneTreeAdaptor->fetch_by_dbID($nc_tree_id) or die "Could not fetch nc_tree with id=$nc_tree_id\n";
$self->param('nc_tree', $nc_tree);
my $model_name = $nc_tree->get_tagvalue('model_name');
$self->param('model_name', $model_name);
my $ss_cons = $nc_tree->get_tagvalue('ss_cons');
$self->param('ss_cons', $ss_cons);
my $input_aln = $self->_fetchMultipleAlignment();
$self->param('input_aln', $input_aln);
my $ss_model_picts_dir = $self->param('ss_picts_dir') . "/" . $model_name;
mkdir($ss_model_picts_dir);
$self->param('ss_model_picts_dir', $ss_model_picts_dir);
return;
}
sub run {
my ($self) = @_;
$self->_dumpMultipleAlignment();
$self->get_plot();
return;
}
sub _fetchMultipleAlignment {
my ($self) = @_;
my $tree = $self->param('nc_tree');
my $sa = $tree->get_SimpleAlign( -id => 'MEMBER' );
return $sa;
}
sub _dumpMultipleAlignment {
my ($self) = @_;
my $aln = $self->param('input_aln');
my $model_name = $self->param('model_name');
my $ss_cons = $self->param('ss_cons');
if ($ss_cons =~ /^\.d+$/) {
$self->input_job->autoflow(0);
$self->complete_early("tree " . $self->param('gene_tree_id') . " has no structure: $ss_cons\n");
}
my $ss_model_picts_dir = $self->param('ss_model_picts_dir');
my $aln_filename = "${ss_model_picts_dir}/${model_name}.sto";
print STDERR "ALN FILE IS: $aln_filename\n" if ($self->debug);
open my $aln_fh, ">", $aln_filename or die $!;
print $aln_fh "# STOCKHOLM 1.0\n";
for my $aln_seq ($aln->each_seq) {
printf $aln_fh ("%-20s %s\n", $aln_seq->display_id, $aln_seq->seq);
}
printf $aln_fh ("%-20s\n", "#=GF R2R keep allpairs");
printf $aln_fh ("%-20s %s\n//\n", "#=GC SS_cons", $ss_cons);
close($aln_fh);
$self->param('aln_file', $aln_filename);
return;
}
sub get_cons_aln {
my ($self) = @_;
my $aln_file = $self->param('aln_file');
my $out_aln_file = $aln_file . ".cons";
## For information about these options, check http://breaker.research.yale.edu/R2R/R2R-manual-1.0.3.pdf";
$self->run_r2r_and_check("--GSC-weighted-consensus", $aln_file, $out_aln_file, "3 0.97 0.9 0.75 4 0.97 0.9 0.75 0.5 0.1");
return;
}
sub get_plot {
my ($self) = @_;
my $r2r_exe = $self->param_required('r2r_exe');
my $aln_file = $self->param('aln_file');
my $tree = $self->param('nc_tree');
my $out_aln_file = $aln_file . ".cons";
$self->get_cons_aln();
## First we create the thumbnails
my $meta_file_thumbnail = $aln_file . "-thumbnail.meta";
my $svg_thumbnail_pic = "${out_aln_file}.thumbnail.svg";
open my $meta_thumbnail_fh, ">", $meta_file_thumbnail or die $!;
print $meta_thumbnail_fh "$out_aln_file\tskeleton-with-pairbonds\n";
close($meta_thumbnail_fh);
$self->run_r2r_and_check("", $meta_file_thumbnail, $svg_thumbnail_pic, "");
my $meta_file = $aln_file . ".meta";
## One svg pic per member
for my $member (@{$tree->get_all_Members}) {
my $seq_member_id = $member->name();
open my $meta_fh, ">", $meta_file or die $!;
print $meta_fh "$out_aln_file\n";
print $meta_fh "$aln_file\toneseq\t$seq_member_id\n";
close($meta_fh);
my $svg_pic_filename = "${out_aln_file}-${seq_member_id}.svg";
$self->run_r2r_and_check("", $meta_file, $svg_pic_filename, "");
}
return;
}
sub fix_aln_file {
my ($self, $msg) = @_;
my @columns = $msg =~ /\[(\d+),(\d+)\]/g;
my $aln_file = $self->param('aln_file');
open my $aln_fh, "<", $aln_file or die $!;
my $label_line = sprintf("%-21s", "#=GC R2R_LABEL");
my $keep_line = sprintf("%-21s\n", "#=GF R2R keep p");
my $new_aln = "";
while (<$aln_fh>) {
$new_aln .= $_;
chomp;
if (/^#=GC\s+SS_cons\s+(.+)$/) {
print STDERR "GC SS_CONS LINE: $_\n";
my $cons_seq_len = length($1);
$label_line .= "." x $cons_seq_len;
for my $pos (@columns) {
substr($label_line, $pos, 1, "p");
}
$new_aln .= "$label_line\n";
$new_aln .= "$keep_line";
}
}
close($aln_fh);
open $aln_fh, ">", $aln_file or die $!;
print $aln_fh $new_aln;
close($aln_fh);
$self->param('fixed_aln', 1);
$self->get_cons_aln();
}
sub run_r2r_and_check {
my ($self, $opts, $infile, $outfile, $extra_params) = @_;
my $r2r_exe = $self->param_required('r2r_exe');
my $cmd = "$r2r_exe $opts $infile $outfile $extra_params";
my $runCmd = $self->run_command($cmd);
if ($runCmd->exit_code) {
if ($self->param('fixed_aln')) {
die "Problem running r2r: " . $runCmd->out . "\n";
} else {
$self->fix_aln_file($runCmd->out);
$self->run_r2r_and_check($opts, $infile, $outfile, $extra_params);
}
}
if (! -e $outfile) {
die "Problem running r2r: $outfile doesn't exist\n";
}
return;
}
1;
| ckongEbi/ensembl-compara | modules/Bio/EnsEMBL/Compara/RunnableDB/ncRNAtrees/GenerateSSPict.pm | Perl | apache-2.0 | 6,773 |
#!/usr/bin/env perl
$number_of_controllers = `arcconf getversion | awk '/^Controllers found:.*\$/{print \$3}'`;
for ($controller = 1; $controller <= $number_of_controllers; $controller++) {
$config = `arcconf getconfig $controller PD`;
foreach ($config =~ /(Device #\d+.+?MaxCache Assigned[^\n]*)/sg) {
if ($_ !~ /Write Cache\s*:\s*Disabled/ && $_ =~ /Reported Channel,Device\(T:L\)\s*:\s*(\d+),(\d+)\(\d+:\d+\)/) {
print "$controller\t$1\t$2\n";
}
}
}
| tomaszdurka/puppet-packages | modules/raid/templates/adaptec/arcconf-write-cache-on-devices.pl | Perl | mit | 464 |
# !!!!!!! DO NOT EDIT THIS FILE !!!!!!!
# This file is machine-generated by lib/unicore/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';
0964 0965
0981 0983
0985 098C
098F 0990
0993 09A8
09AA 09B0
09B2
09B6 09B9
09BC 09C4
09C7 09C8
09CB 09CE
09D7
09DC 09DD
09DF 09E3
09E6 09FB
END
| efortuna/AndroidSDKClone | ndk_experimental/prebuilt/linux-x86_64/lib/perl5/5.16.2/unicore/lib/Scx/Beng.pl | Perl | apache-2.0 | 567 |
#!/usr/bin/env perl
# ====================================================================
# Written by Andy Polyakov <appro@fy.chalmers.se> for the OpenSSL
# project. The module is, however, dual licensed under OpenSSL and
# CRYPTOGAMS licenses depending on where you obtain it. For further
# details see http://www.openssl.org/~appro/cryptogams/.
# ====================================================================
# October 2005
#
# "Teaser" Montgomery multiplication module for UltraSPARC. Why FPU?
# Because unlike integer multiplier, which simply stalls whole CPU,
# FPU is fully pipelined and can effectively emit 48 bit partial
# product every cycle. Why not blended SPARC v9? One can argue that
# making this module dependent on UltraSPARC VIS extension limits its
# binary compatibility. Well yes, it does exclude SPARC64 prior-V(!)
# implementations from compatibility matrix. But the rest, whole Sun
# UltraSPARC family and brand new Fujitsu's SPARC64 V, all support
# VIS extension instructions used in this module. This is considered
# good enough to not care about HAL SPARC64 users [if any] who have
# integer-only pure SPARCv9 module to "fall down" to.
# USI&II cores currently exhibit uniform 2x improvement [over pre-
# bn_mul_mont codebase] for all key lengths and benchmarks. On USIII
# performance improves few percents for shorter keys and worsens few
# percents for longer keys. This is because USIII integer multiplier
# is >3x faster than USI&II one, which is harder to match [but see
# TODO list below]. It should also be noted that SPARC64 V features
# out-of-order execution, which *might* mean that integer multiplier
# is pipelined, which in turn *might* be impossible to match... On
# additional note, SPARC64 V implements FP Multiply-Add instruction,
# which is perfectly usable in this context... In other words, as far
# as Fujitsu SPARC64 V goes, talk to the author:-)
# The implementation implies following "non-natural" limitations on
# input arguments:
# - num may not be less than 4;
# - num has to be even;
# Failure to meet either condition has no fatal effects, simply
# doesn't give any performance gain.
# TODO:
# - modulo-schedule inner loop for better performance (on in-order
# execution core such as UltraSPARC this shall result in further
# noticeable(!) improvement);
# - dedicated squaring procedure[?];
######################################################################
# November 2006
#
# Modulo-scheduled inner loops allow to interleave floating point and
# integer instructions and minimize Read-After-Write penalties. This
# results in *further* 20-50% perfromance improvement [depending on
# key length, more for longer keys] on USI&II cores and 30-80% - on
# USIII&IV.
$fname="bn_mul_mont_fpu";
$bits=32;
for (@ARGV) { $bits=64 if (/\-m64/ || /\-xarch\=v9/); }
if ($bits==64) {
$bias=2047;
$frame=192;
} else {
$bias=0;
$frame=128; # 96 rounded up to largest known cache-line
}
$locals=64;
# In order to provide for 32-/64-bit ABI duality, I keep integers wider
# than 32 bit in %g1-%g4 and %o0-%o5. %l0-%l7 and %i0-%i5 are used
# exclusively for pointers, indexes and other small values...
# int bn_mul_mont(
$rp="%i0"; # BN_ULONG *rp,
$ap="%i1"; # const BN_ULONG *ap,
$bp="%i2"; # const BN_ULONG *bp,
$np="%i3"; # const BN_ULONG *np,
$n0="%i4"; # const BN_ULONG *n0,
$num="%i5"; # int num);
$tp="%l0"; # t[num]
$ap_l="%l1"; # a[num],n[num] are smashed to 32-bit words and saved
$ap_h="%l2"; # to these four vectors as double-precision FP values.
$np_l="%l3"; # This way a bunch of fxtods are eliminated in second
$np_h="%l4"; # loop and L1-cache aliasing is minimized...
$i="%l5";
$j="%l6";
$mask="%l7"; # 16-bit mask, 0xffff
$n0="%g4"; # reassigned(!) to "64-bit" register
$carry="%i4"; # %i4 reused(!) for a carry bit
# FP register naming chart
#
# ..HILO
# dcba
# --------
# LOa
# LOb
# LOc
# LOd
# HIa
# HIb
# HIc
# HId
# ..a
# ..b
$ba="%f0"; $bb="%f2"; $bc="%f4"; $bd="%f6";
$na="%f8"; $nb="%f10"; $nc="%f12"; $nd="%f14";
$alo="%f16"; $alo_="%f17"; $ahi="%f18"; $ahi_="%f19";
$nlo="%f20"; $nlo_="%f21"; $nhi="%f22"; $nhi_="%f23";
$dota="%f24"; $dotb="%f26";
$aloa="%f32"; $alob="%f34"; $aloc="%f36"; $alod="%f38";
$ahia="%f40"; $ahib="%f42"; $ahic="%f44"; $ahid="%f46";
$nloa="%f48"; $nlob="%f50"; $nloc="%f52"; $nlod="%f54";
$nhia="%f56"; $nhib="%f58"; $nhic="%f60"; $nhid="%f62";
$ASI_FL16_P=0xD2; # magic ASI value to engage 16-bit FP load
$code=<<___;
.section ".text",#alloc,#execinstr
.global $fname
.align 32
$fname:
save %sp,-$frame-$locals,%sp
cmp $num,4
bl,a,pn %icc,.Lret
clr %i0
andcc $num,1,%g0 ! $num has to be even...
bnz,a,pn %icc,.Lret
clr %i0 ! signal "unsupported input value"
srl $num,1,$num
sethi %hi(0xffff),$mask
ld [%i4+0],$n0 ! $n0 reassigned, remember?
or $mask,%lo(0xffff),$mask
ld [%i4+4],%o0
sllx %o0,32,%o0
or %o0,$n0,$n0 ! $n0=n0[1].n0[0]
sll $num,3,$num ! num*=8
add %sp,$bias,%o0 ! real top of stack
sll $num,2,%o1
add %o1,$num,%o1 ! %o1=num*5
sub %o0,%o1,%o0
and %o0,-2048,%o0 ! optimize TLB utilization
sub %o0,$bias,%sp ! alloca(5*num*8)
rd %asi,%o7 ! save %asi
add %sp,$bias+$frame+$locals,$tp
add $tp,$num,$ap_l
add $ap_l,$num,$ap_l ! [an]p_[lh] point at the vectors' ends !
add $ap_l,$num,$ap_h
add $ap_h,$num,$np_l
add $np_l,$num,$np_h
wr %g0,$ASI_FL16_P,%asi ! setup %asi for 16-bit FP loads
add $rp,$num,$rp ! readjust input pointers to point
add $ap,$num,$ap ! at the ends too...
add $bp,$num,$bp
add $np,$num,$np
stx %o7,[%sp+$bias+$frame+48] ! save %asi
sub %g0,$num,$i ! i=-num
sub %g0,$num,$j ! j=-num
add $ap,$j,%o3
add $bp,$i,%o4
ld [%o3+4],%g1 ! bp[0]
ld [%o3+0],%o0
ld [%o4+4],%g5 ! ap[0]
sllx %g1,32,%g1
ld [%o4+0],%o1
sllx %g5,32,%g5
or %g1,%o0,%o0
or %g5,%o1,%o1
add $np,$j,%o5
mulx %o1,%o0,%o0 ! ap[0]*bp[0]
mulx $n0,%o0,%o0 ! ap[0]*bp[0]*n0
stx %o0,[%sp+$bias+$frame+0]
ld [%o3+0],$alo_ ! load a[j] as pair of 32-bit words
fzeros $alo
ld [%o3+4],$ahi_
fzeros $ahi
ld [%o5+0],$nlo_ ! load n[j] as pair of 32-bit words
fzeros $nlo
ld [%o5+4],$nhi_
fzeros $nhi
! transfer b[i] to FPU as 4x16-bit values
ldda [%o4+2]%asi,$ba
fxtod $alo,$alo
ldda [%o4+0]%asi,$bb
fxtod $ahi,$ahi
ldda [%o4+6]%asi,$bc
fxtod $nlo,$nlo
ldda [%o4+4]%asi,$bd
fxtod $nhi,$nhi
! transfer ap[0]*b[0]*n0 to FPU as 4x16-bit values
ldda [%sp+$bias+$frame+6]%asi,$na
fxtod $ba,$ba
ldda [%sp+$bias+$frame+4]%asi,$nb
fxtod $bb,$bb
ldda [%sp+$bias+$frame+2]%asi,$nc
fxtod $bc,$bc
ldda [%sp+$bias+$frame+0]%asi,$nd
fxtod $bd,$bd
std $alo,[$ap_l+$j] ! save smashed ap[j] in double format
fxtod $na,$na
std $ahi,[$ap_h+$j]
fxtod $nb,$nb
std $nlo,[$np_l+$j] ! save smashed np[j] in double format
fxtod $nc,$nc
std $nhi,[$np_h+$j]
fxtod $nd,$nd
fmuld $alo,$ba,$aloa
fmuld $nlo,$na,$nloa
fmuld $alo,$bb,$alob
fmuld $nlo,$nb,$nlob
fmuld $alo,$bc,$aloc
faddd $aloa,$nloa,$nloa
fmuld $nlo,$nc,$nloc
fmuld $alo,$bd,$alod
faddd $alob,$nlob,$nlob
fmuld $nlo,$nd,$nlod
fmuld $ahi,$ba,$ahia
faddd $aloc,$nloc,$nloc
fmuld $nhi,$na,$nhia
fmuld $ahi,$bb,$ahib
faddd $alod,$nlod,$nlod
fmuld $nhi,$nb,$nhib
fmuld $ahi,$bc,$ahic
faddd $ahia,$nhia,$nhia
fmuld $nhi,$nc,$nhic
fmuld $ahi,$bd,$ahid
faddd $ahib,$nhib,$nhib
fmuld $nhi,$nd,$nhid
faddd $ahic,$nhic,$dota ! $nhic
faddd $ahid,$nhid,$dotb ! $nhid
faddd $nloc,$nhia,$nloc
faddd $nlod,$nhib,$nlod
fdtox $nloa,$nloa
fdtox $nlob,$nlob
fdtox $nloc,$nloc
fdtox $nlod,$nlod
std $nloa,[%sp+$bias+$frame+0]
add $j,8,$j
std $nlob,[%sp+$bias+$frame+8]
add $ap,$j,%o4
std $nloc,[%sp+$bias+$frame+16]
add $np,$j,%o5
std $nlod,[%sp+$bias+$frame+24]
ld [%o4+0],$alo_ ! load a[j] as pair of 32-bit words
fzeros $alo
ld [%o4+4],$ahi_
fzeros $ahi
ld [%o5+0],$nlo_ ! load n[j] as pair of 32-bit words
fzeros $nlo
ld [%o5+4],$nhi_
fzeros $nhi
fxtod $alo,$alo
fxtod $ahi,$ahi
fxtod $nlo,$nlo
fxtod $nhi,$nhi
ldx [%sp+$bias+$frame+0],%o0
fmuld $alo,$ba,$aloa
ldx [%sp+$bias+$frame+8],%o1
fmuld $nlo,$na,$nloa
ldx [%sp+$bias+$frame+16],%o2
fmuld $alo,$bb,$alob
ldx [%sp+$bias+$frame+24],%o3
fmuld $nlo,$nb,$nlob
srlx %o0,16,%o7
std $alo,[$ap_l+$j] ! save smashed ap[j] in double format
fmuld $alo,$bc,$aloc
add %o7,%o1,%o1
std $ahi,[$ap_h+$j]
faddd $aloa,$nloa,$nloa
fmuld $nlo,$nc,$nloc
srlx %o1,16,%o7
std $nlo,[$np_l+$j] ! save smashed np[j] in double format
fmuld $alo,$bd,$alod
add %o7,%o2,%o2
std $nhi,[$np_h+$j]
faddd $alob,$nlob,$nlob
fmuld $nlo,$nd,$nlod
srlx %o2,16,%o7
fmuld $ahi,$ba,$ahia
add %o7,%o3,%o3 ! %o3.%o2[0..15].%o1[0..15].%o0[0..15]
faddd $aloc,$nloc,$nloc
fmuld $nhi,$na,$nhia
!and %o0,$mask,%o0
!and %o1,$mask,%o1
!and %o2,$mask,%o2
!sllx %o1,16,%o1
!sllx %o2,32,%o2
!sllx %o3,48,%o7
!or %o1,%o0,%o0
!or %o2,%o0,%o0
!or %o7,%o0,%o0 ! 64-bit result
srlx %o3,16,%g1 ! 34-bit carry
fmuld $ahi,$bb,$ahib
faddd $alod,$nlod,$nlod
fmuld $nhi,$nb,$nhib
fmuld $ahi,$bc,$ahic
faddd $ahia,$nhia,$nhia
fmuld $nhi,$nc,$nhic
fmuld $ahi,$bd,$ahid
faddd $ahib,$nhib,$nhib
fmuld $nhi,$nd,$nhid
faddd $dota,$nloa,$nloa
faddd $dotb,$nlob,$nlob
faddd $ahic,$nhic,$dota ! $nhic
faddd $ahid,$nhid,$dotb ! $nhid
faddd $nloc,$nhia,$nloc
faddd $nlod,$nhib,$nlod
fdtox $nloa,$nloa
fdtox $nlob,$nlob
fdtox $nloc,$nloc
fdtox $nlod,$nlod
std $nloa,[%sp+$bias+$frame+0]
std $nlob,[%sp+$bias+$frame+8]
addcc $j,8,$j
std $nloc,[%sp+$bias+$frame+16]
bz,pn %icc,.L1stskip
std $nlod,[%sp+$bias+$frame+24]
.align 32 ! incidentally already aligned !
.L1st:
add $ap,$j,%o4
add $np,$j,%o5
ld [%o4+0],$alo_ ! load a[j] as pair of 32-bit words
fzeros $alo
ld [%o4+4],$ahi_
fzeros $ahi
ld [%o5+0],$nlo_ ! load n[j] as pair of 32-bit words
fzeros $nlo
ld [%o5+4],$nhi_
fzeros $nhi
fxtod $alo,$alo
fxtod $ahi,$ahi
fxtod $nlo,$nlo
fxtod $nhi,$nhi
ldx [%sp+$bias+$frame+0],%o0
fmuld $alo,$ba,$aloa
ldx [%sp+$bias+$frame+8],%o1
fmuld $nlo,$na,$nloa
ldx [%sp+$bias+$frame+16],%o2
fmuld $alo,$bb,$alob
ldx [%sp+$bias+$frame+24],%o3
fmuld $nlo,$nb,$nlob
srlx %o0,16,%o7
std $alo,[$ap_l+$j] ! save smashed ap[j] in double format
fmuld $alo,$bc,$aloc
add %o7,%o1,%o1
std $ahi,[$ap_h+$j]
faddd $aloa,$nloa,$nloa
fmuld $nlo,$nc,$nloc
srlx %o1,16,%o7
std $nlo,[$np_l+$j] ! save smashed np[j] in double format
fmuld $alo,$bd,$alod
add %o7,%o2,%o2
std $nhi,[$np_h+$j]
faddd $alob,$nlob,$nlob
fmuld $nlo,$nd,$nlod
srlx %o2,16,%o7
fmuld $ahi,$ba,$ahia
add %o7,%o3,%o3 ! %o3.%o2[0..15].%o1[0..15].%o0[0..15]
and %o0,$mask,%o0
faddd $aloc,$nloc,$nloc
fmuld $nhi,$na,$nhia
and %o1,$mask,%o1
and %o2,$mask,%o2
fmuld $ahi,$bb,$ahib
sllx %o1,16,%o1
faddd $alod,$nlod,$nlod
fmuld $nhi,$nb,$nhib
sllx %o2,32,%o2
fmuld $ahi,$bc,$ahic
sllx %o3,48,%o7
or %o1,%o0,%o0
faddd $ahia,$nhia,$nhia
fmuld $nhi,$nc,$nhic
or %o2,%o0,%o0
fmuld $ahi,$bd,$ahid
or %o7,%o0,%o0 ! 64-bit result
faddd $ahib,$nhib,$nhib
fmuld $nhi,$nd,$nhid
addcc %g1,%o0,%o0
faddd $dota,$nloa,$nloa
srlx %o3,16,%g1 ! 34-bit carry
faddd $dotb,$nlob,$nlob
bcs,a %xcc,.+8
add %g1,1,%g1
stx %o0,[$tp] ! tp[j-1]=
faddd $ahic,$nhic,$dota ! $nhic
faddd $ahid,$nhid,$dotb ! $nhid
faddd $nloc,$nhia,$nloc
faddd $nlod,$nhib,$nlod
fdtox $nloa,$nloa
fdtox $nlob,$nlob
fdtox $nloc,$nloc
fdtox $nlod,$nlod
std $nloa,[%sp+$bias+$frame+0]
std $nlob,[%sp+$bias+$frame+8]
std $nloc,[%sp+$bias+$frame+16]
std $nlod,[%sp+$bias+$frame+24]
addcc $j,8,$j
bnz,pt %icc,.L1st
add $tp,8,$tp
.L1stskip:
fdtox $dota,$dota
fdtox $dotb,$dotb
ldx [%sp+$bias+$frame+0],%o0
ldx [%sp+$bias+$frame+8],%o1
ldx [%sp+$bias+$frame+16],%o2
ldx [%sp+$bias+$frame+24],%o3
srlx %o0,16,%o7
std $dota,[%sp+$bias+$frame+32]
add %o7,%o1,%o1
std $dotb,[%sp+$bias+$frame+40]
srlx %o1,16,%o7
add %o7,%o2,%o2
srlx %o2,16,%o7
add %o7,%o3,%o3 ! %o3.%o2[0..15].%o1[0..15].%o0[0..15]
and %o0,$mask,%o0
and %o1,$mask,%o1
and %o2,$mask,%o2
sllx %o1,16,%o1
sllx %o2,32,%o2
sllx %o3,48,%o7
or %o1,%o0,%o0
or %o2,%o0,%o0
or %o7,%o0,%o0 ! 64-bit result
ldx [%sp+$bias+$frame+32],%o4
addcc %g1,%o0,%o0
ldx [%sp+$bias+$frame+40],%o5
srlx %o3,16,%g1 ! 34-bit carry
bcs,a %xcc,.+8
add %g1,1,%g1
stx %o0,[$tp] ! tp[j-1]=
add $tp,8,$tp
srlx %o4,16,%o7
add %o7,%o5,%o5
and %o4,$mask,%o4
sllx %o5,16,%o7
or %o7,%o4,%o4
addcc %g1,%o4,%o4
srlx %o5,48,%g1
bcs,a %xcc,.+8
add %g1,1,%g1
mov %g1,$carry
stx %o4,[$tp] ! tp[num-1]=
ba .Louter
add $i,8,$i
.align 32
.Louter:
sub %g0,$num,$j ! j=-num
add %sp,$bias+$frame+$locals,$tp
add $ap,$j,%o3
add $bp,$i,%o4
ld [%o3+4],%g1 ! bp[i]
ld [%o3+0],%o0
ld [%o4+4],%g5 ! ap[0]
sllx %g1,32,%g1
ld [%o4+0],%o1
sllx %g5,32,%g5
or %g1,%o0,%o0
or %g5,%o1,%o1
ldx [$tp],%o2 ! tp[0]
mulx %o1,%o0,%o0
addcc %o2,%o0,%o0
mulx $n0,%o0,%o0 ! (ap[0]*bp[i]+t[0])*n0
stx %o0,[%sp+$bias+$frame+0]
! transfer b[i] to FPU as 4x16-bit values
ldda [%o4+2]%asi,$ba
ldda [%o4+0]%asi,$bb
ldda [%o4+6]%asi,$bc
ldda [%o4+4]%asi,$bd
! transfer (ap[0]*b[i]+t[0])*n0 to FPU as 4x16-bit values
ldda [%sp+$bias+$frame+6]%asi,$na
fxtod $ba,$ba
ldda [%sp+$bias+$frame+4]%asi,$nb
fxtod $bb,$bb
ldda [%sp+$bias+$frame+2]%asi,$nc
fxtod $bc,$bc
ldda [%sp+$bias+$frame+0]%asi,$nd
fxtod $bd,$bd
ldd [$ap_l+$j],$alo ! load a[j] in double format
fxtod $na,$na
ldd [$ap_h+$j],$ahi
fxtod $nb,$nb
ldd [$np_l+$j],$nlo ! load n[j] in double format
fxtod $nc,$nc
ldd [$np_h+$j],$nhi
fxtod $nd,$nd
fmuld $alo,$ba,$aloa
fmuld $nlo,$na,$nloa
fmuld $alo,$bb,$alob
fmuld $nlo,$nb,$nlob
fmuld $alo,$bc,$aloc
faddd $aloa,$nloa,$nloa
fmuld $nlo,$nc,$nloc
fmuld $alo,$bd,$alod
faddd $alob,$nlob,$nlob
fmuld $nlo,$nd,$nlod
fmuld $ahi,$ba,$ahia
faddd $aloc,$nloc,$nloc
fmuld $nhi,$na,$nhia
fmuld $ahi,$bb,$ahib
faddd $alod,$nlod,$nlod
fmuld $nhi,$nb,$nhib
fmuld $ahi,$bc,$ahic
faddd $ahia,$nhia,$nhia
fmuld $nhi,$nc,$nhic
fmuld $ahi,$bd,$ahid
faddd $ahib,$nhib,$nhib
fmuld $nhi,$nd,$nhid
faddd $ahic,$nhic,$dota ! $nhic
faddd $ahid,$nhid,$dotb ! $nhid
faddd $nloc,$nhia,$nloc
faddd $nlod,$nhib,$nlod
fdtox $nloa,$nloa
fdtox $nlob,$nlob
fdtox $nloc,$nloc
fdtox $nlod,$nlod
std $nloa,[%sp+$bias+$frame+0]
std $nlob,[%sp+$bias+$frame+8]
std $nloc,[%sp+$bias+$frame+16]
add $j,8,$j
std $nlod,[%sp+$bias+$frame+24]
ldd [$ap_l+$j],$alo ! load a[j] in double format
ldd [$ap_h+$j],$ahi
ldd [$np_l+$j],$nlo ! load n[j] in double format
ldd [$np_h+$j],$nhi
fmuld $alo,$ba,$aloa
fmuld $nlo,$na,$nloa
fmuld $alo,$bb,$alob
fmuld $nlo,$nb,$nlob
fmuld $alo,$bc,$aloc
ldx [%sp+$bias+$frame+0],%o0
faddd $aloa,$nloa,$nloa
fmuld $nlo,$nc,$nloc
ldx [%sp+$bias+$frame+8],%o1
fmuld $alo,$bd,$alod
ldx [%sp+$bias+$frame+16],%o2
faddd $alob,$nlob,$nlob
fmuld $nlo,$nd,$nlod
ldx [%sp+$bias+$frame+24],%o3
fmuld $ahi,$ba,$ahia
srlx %o0,16,%o7
faddd $aloc,$nloc,$nloc
fmuld $nhi,$na,$nhia
add %o7,%o1,%o1
fmuld $ahi,$bb,$ahib
srlx %o1,16,%o7
faddd $alod,$nlod,$nlod
fmuld $nhi,$nb,$nhib
add %o7,%o2,%o2
fmuld $ahi,$bc,$ahic
srlx %o2,16,%o7
faddd $ahia,$nhia,$nhia
fmuld $nhi,$nc,$nhic
add %o7,%o3,%o3 ! %o3.%o2[0..15].%o1[0..15].%o0[0..15]
! why?
and %o0,$mask,%o0
fmuld $ahi,$bd,$ahid
and %o1,$mask,%o1
and %o2,$mask,%o2
faddd $ahib,$nhib,$nhib
fmuld $nhi,$nd,$nhid
sllx %o1,16,%o1
faddd $dota,$nloa,$nloa
sllx %o2,32,%o2
faddd $dotb,$nlob,$nlob
sllx %o3,48,%o7
or %o1,%o0,%o0
faddd $ahic,$nhic,$dota ! $nhic
or %o2,%o0,%o0
faddd $ahid,$nhid,$dotb ! $nhid
or %o7,%o0,%o0 ! 64-bit result
ldx [$tp],%o7
faddd $nloc,$nhia,$nloc
addcc %o7,%o0,%o0
! end-of-why?
faddd $nlod,$nhib,$nlod
srlx %o3,16,%g1 ! 34-bit carry
fdtox $nloa,$nloa
bcs,a %xcc,.+8
add %g1,1,%g1
fdtox $nlob,$nlob
fdtox $nloc,$nloc
fdtox $nlod,$nlod
std $nloa,[%sp+$bias+$frame+0]
std $nlob,[%sp+$bias+$frame+8]
addcc $j,8,$j
std $nloc,[%sp+$bias+$frame+16]
bz,pn %icc,.Linnerskip
std $nlod,[%sp+$bias+$frame+24]
ba .Linner
nop
.align 32
.Linner:
ldd [$ap_l+$j],$alo ! load a[j] in double format
ldd [$ap_h+$j],$ahi
ldd [$np_l+$j],$nlo ! load n[j] in double format
ldd [$np_h+$j],$nhi
fmuld $alo,$ba,$aloa
fmuld $nlo,$na,$nloa
fmuld $alo,$bb,$alob
fmuld $nlo,$nb,$nlob
fmuld $alo,$bc,$aloc
ldx [%sp+$bias+$frame+0],%o0
faddd $aloa,$nloa,$nloa
fmuld $nlo,$nc,$nloc
ldx [%sp+$bias+$frame+8],%o1
fmuld $alo,$bd,$alod
ldx [%sp+$bias+$frame+16],%o2
faddd $alob,$nlob,$nlob
fmuld $nlo,$nd,$nlod
ldx [%sp+$bias+$frame+24],%o3
fmuld $ahi,$ba,$ahia
srlx %o0,16,%o7
faddd $aloc,$nloc,$nloc
fmuld $nhi,$na,$nhia
add %o7,%o1,%o1
fmuld $ahi,$bb,$ahib
srlx %o1,16,%o7
faddd $alod,$nlod,$nlod
fmuld $nhi,$nb,$nhib
add %o7,%o2,%o2
fmuld $ahi,$bc,$ahic
srlx %o2,16,%o7
faddd $ahia,$nhia,$nhia
fmuld $nhi,$nc,$nhic
add %o7,%o3,%o3 ! %o3.%o2[0..15].%o1[0..15].%o0[0..15]
and %o0,$mask,%o0
fmuld $ahi,$bd,$ahid
and %o1,$mask,%o1
and %o2,$mask,%o2
faddd $ahib,$nhib,$nhib
fmuld $nhi,$nd,$nhid
sllx %o1,16,%o1
faddd $dota,$nloa,$nloa
sllx %o2,32,%o2
faddd $dotb,$nlob,$nlob
sllx %o3,48,%o7
or %o1,%o0,%o0
faddd $ahic,$nhic,$dota ! $nhic
or %o2,%o0,%o0
faddd $ahid,$nhid,$dotb ! $nhid
or %o7,%o0,%o0 ! 64-bit result
faddd $nloc,$nhia,$nloc
addcc %g1,%o0,%o0
ldx [$tp+8],%o7 ! tp[j]
faddd $nlod,$nhib,$nlod
srlx %o3,16,%g1 ! 34-bit carry
fdtox $nloa,$nloa
bcs,a %xcc,.+8
add %g1,1,%g1
fdtox $nlob,$nlob
addcc %o7,%o0,%o0
fdtox $nloc,$nloc
bcs,a %xcc,.+8
add %g1,1,%g1
stx %o0,[$tp] ! tp[j-1]
fdtox $nlod,$nlod
std $nloa,[%sp+$bias+$frame+0]
std $nlob,[%sp+$bias+$frame+8]
std $nloc,[%sp+$bias+$frame+16]
addcc $j,8,$j
std $nlod,[%sp+$bias+$frame+24]
bnz,pt %icc,.Linner
add $tp,8,$tp
.Linnerskip:
fdtox $dota,$dota
fdtox $dotb,$dotb
ldx [%sp+$bias+$frame+0],%o0
ldx [%sp+$bias+$frame+8],%o1
ldx [%sp+$bias+$frame+16],%o2
ldx [%sp+$bias+$frame+24],%o3
srlx %o0,16,%o7
std $dota,[%sp+$bias+$frame+32]
add %o7,%o1,%o1
std $dotb,[%sp+$bias+$frame+40]
srlx %o1,16,%o7
add %o7,%o2,%o2
srlx %o2,16,%o7
add %o7,%o3,%o3 ! %o3.%o2[0..15].%o1[0..15].%o0[0..15]
and %o0,$mask,%o0
and %o1,$mask,%o1
and %o2,$mask,%o2
sllx %o1,16,%o1
sllx %o2,32,%o2
sllx %o3,48,%o7
or %o1,%o0,%o0
or %o2,%o0,%o0
ldx [%sp+$bias+$frame+32],%o4
or %o7,%o0,%o0 ! 64-bit result
ldx [%sp+$bias+$frame+40],%o5
addcc %g1,%o0,%o0
ldx [$tp+8],%o7 ! tp[j]
srlx %o3,16,%g1 ! 34-bit carry
bcs,a %xcc,.+8
add %g1,1,%g1
addcc %o7,%o0,%o0
bcs,a %xcc,.+8
add %g1,1,%g1
stx %o0,[$tp] ! tp[j-1]
add $tp,8,$tp
srlx %o4,16,%o7
add %o7,%o5,%o5
and %o4,$mask,%o4
sllx %o5,16,%o7
or %o7,%o4,%o4
addcc %g1,%o4,%o4
srlx %o5,48,%g1
bcs,a %xcc,.+8
add %g1,1,%g1
addcc $carry,%o4,%o4
stx %o4,[$tp] ! tp[num-1]
mov %g1,$carry
bcs,a %xcc,.+8
add $carry,1,$carry
addcc $i,8,$i
bnz %icc,.Louter
nop
add $tp,8,$tp ! adjust tp to point at the end
orn %g0,%g0,%g4
sub %g0,$num,%o7 ! n=-num
ba .Lsub
subcc %g0,%g0,%g0 ! clear %icc.c
.align 32
.Lsub:
ldx [$tp+%o7],%o0
add $np,%o7,%g1
ld [%g1+0],%o2
ld [%g1+4],%o3
srlx %o0,32,%o1
subccc %o0,%o2,%o2
add $rp,%o7,%g1
subccc %o1,%o3,%o3
st %o2,[%g1+0]
add %o7,8,%o7
brnz,pt %o7,.Lsub
st %o3,[%g1+4]
subc $carry,0,%g4
sub %g0,$num,%o7 ! n=-num
ba .Lcopy
nop
.align 32
.Lcopy:
ldx [$tp+%o7],%o0
add $rp,%o7,%g1
ld [%g1+0],%o2
ld [%g1+4],%o3
stx %g0,[$tp+%o7]
and %o0,%g4,%o0
srlx %o0,32,%o1
andn %o2,%g4,%o2
andn %o3,%g4,%o3
or %o2,%o0,%o0
or %o3,%o1,%o1
st %o0,[%g1+0]
add %o7,8,%o7
brnz,pt %o7,.Lcopy
st %o1,[%g1+4]
sub %g0,$num,%o7 ! n=-num
.Lzap:
stx %g0,[$ap_l+%o7]
stx %g0,[$ap_h+%o7]
stx %g0,[$np_l+%o7]
stx %g0,[$np_h+%o7]
add %o7,8,%o7
brnz,pt %o7,.Lzap
nop
ldx [%sp+$bias+$frame+48],%o7
wr %g0,%o7,%asi ! restore %asi
mov 1,%i0
.Lret:
ret
restore
.type $fname,#function
.size $fname,(.-$fname)
.asciz "Montgomery Multipltication for UltraSPARC, CRYPTOGAMS by <appro\@openssl.org>"
.align 32
___
$code =~ s/\`([^\`]*)\`/eval($1)/gem;
# Below substitution makes it possible to compile without demanding
# VIS extentions on command line, e.g. -xarch=v9 vs. -xarch=v9a. I
# dare to do this, because VIS capability is detected at run-time now
# and this routine is not called on CPU not capable to execute it. Do
# note that fzeros is not the only VIS dependency! Another dependency
# is implicit and is just _a_ numerical value loaded to %asi register,
# which assembler can't recognize as VIS specific...
$code =~ s/fzeros\s+%f([0-9]+)/
sprintf(".word\t0x%x\t! fzeros %%f%d",0x81b00c20|($1<<25),$1)
/gem;
print $code;
# flush
close STDOUT;
| caidongyun/nginx-openresty-windows | nginx/objs/lib/openssl-1.0.1g/crypto/bn/asm/sparcv9a-mont.pl | Perl | bsd-2-clause | 21,605 |
########################################################################
# Bio::KBase::ObjectAPI::KBaseOntology::Role - This is the moose object corresponding to the Role object
# Authors: Christopher Henry, Scott Devoid, Paul Frybarger
# Contact email: chenry@mcs.anl.gov
# Development location: Mathematics and Computer Science Division, Argonne National Lab
# Date of module creation: 2012-03-26T23:22:35
########################################################################
use strict;
use Bio::KBase::ObjectAPI::KBaseOntology::DB::Role;
package Bio::KBase::ObjectAPI::KBaseOntology::Role;
use Moose;
use namespace::autoclean;
extends 'Bio::KBase::ObjectAPI::KBaseOntology::DB::Role';
#***********************************************************************************************************
# ADDITIONAL ATTRIBUTES:
#***********************************************************************************************************
has searchname => ( is => 'rw', isa => 'Str',printOrder => '-1', type => 'msdata', metaclass => 'Typed', lazy => 1, builder => '_buildsearchname' );
has reactions => ( is => 'rw', isa => 'Str',printOrder => '-1', type => 'msdata', metaclass => 'Typed', lazy => 1, builder => '_buildreactions' );
has complexIDs => ( is => 'rw', isa => 'ArrayRef',printOrder => '-1', type => 'msdata', metaclass => 'Typed', lazy => 1, builder => '_buildcomplexIDs' );
#***********************************************************************************************************
# BUILDERS:
#***********************************************************************************************************
sub _buildsearchname {
my ($self) = @_;
return Bio::KBase::ObjectAPI::utilities::convertRoleToSearchRole($self->name());
}
sub _buildreactions {
my ($self) = @_;
my $hash = $self->parent()->roleReactionHash();
my $rxnlist = "";
if (defined($hash->{$self->uuid()})) {
foreach my $rxn (keys(%{$hash->{$self->uuid()}})) {
if (length($rxnlist) > 0) {
$rxnlist .= ";";
}
$rxnlist .= $hash->{$self->uuid()}->{$rxn}->id();
}
}
return $rxnlist;
}
sub _buildcomplexIDs {
my ($self) = @_;
my $hash = $self->parent()->roleComplexHash();
my $complexes = [];
if (defined($hash->{$self->uuid()})) {
foreach my $cpxid (keys(%{$hash->{$self->uuid()}})) {
push(@{$complexes},$hash->{$self->uuid()}->{$cpxid}->id());
}
}
return $complexes;
}
#***********************************************************************************************************
# CONSTANTS:
#***********************************************************************************************************
#***********************************************************************************************************
# FUNCTIONS:
#***********************************************************************************************************
sub getAlias {
my ($self,$set) = @_;
my $aliases = $self->getAliases($set);
return (@$aliases) ? $aliases->[0] : undef;
}
sub getAliases {
my ($self,$setName) = @_;
return [] unless(defined($setName));
my $output = [];
my $aliases = $self->parent()->role_aliases()->{$self->id()};
if (defined($aliases) && defined($aliases->{$setName})) {
return $aliases->{$setName};
}
return $output;
}
sub allAliases {
my ($self) = @_;
my $output = [];
my $aliases = $self->parent()->role_aliases()->{$self->id()};
if (defined($aliases)) {
foreach my $set (keys(%{$aliases})) {
push(@{$output},@{$aliases->{$set}});
}
}
return $output;
}
sub hasAlias {
my ($self,$alias,$setName) = @_;
my $aliases = $self->parent()->role_aliases()->{$self->id()};
if (defined($aliases) && defined($aliases->{$setName})) {
foreach my $searchalias (@{$aliases->{$setName}}) {
if ($searchalias eq $alias) {
return 1;
}
}
}
return 0;
}
__PACKAGE__->meta->make_immutable;
1;
| samseaver/KBaseFBAModeling | lib/Bio/KBase/ObjectAPI/KBaseOntology/Role.pm | Perl | mit | 3,918 |
#!/usr/bin/perl -w
#
# Copyright (C) 2010 Chris Jerdonek (cjerdonek@webkit.org)
#
# 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 APPLE INC. AND ITS 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 APPLE INC. OR ITS 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.
# Unit tests of prepareParsedPatch().
use strict;
use warnings;
use Test::More;
use VCSUtils;
my $diffHashRef1 = { # not a copy, no source revision
copiedFromPath => undef,
indexPath => "indexPath1",
sourceRevision => undef,
svnConvertedText => "diff1",
};
my $diffHashRef2 = { # not a copy, has source revision
copiedFromPath => undef,
indexPath => "indexPath2",
sourceRevision => 20,
svnConvertedText => "diff2",
};
my $diffHashRef3 = { # a copy (copies always have source revision)
copiedFromPath => "sourcePath3",
indexPath => "indexPath2", # Deliberately choosing same as $diffHashRef2
sourceRevision => 3,
svnConvertedText => "diff3",
};
my @testCases = (
{
# New test
testName => "zero diffs: empty array",
diffHashRefsInput => [],
expected => {
copyDiffHashRefs => [],
nonCopyDiffHashRefs => [],
sourceRevisionHash => {},
},
},
{
# New test
testName => "one diff: non-copy, no revision",
diffHashRefsInput => [$diffHashRef1],
expected => {
copyDiffHashRefs => [],
nonCopyDiffHashRefs => [$diffHashRef1],
sourceRevisionHash => {},
},
},
{
# New test
testName => "one diff: non-copy, has revision",
diffHashRefsInput => [$diffHashRef2],
expected => {
copyDiffHashRefs => [],
nonCopyDiffHashRefs => [$diffHashRef2],
sourceRevisionHash => {
"indexPath2" => 20,
}
},
},
{
# New test
testName => "one diff: copy (has revision)",
diffHashRefsInput => [$diffHashRef3],
expected => {
copyDiffHashRefs => [$diffHashRef3],
nonCopyDiffHashRefs => [],
sourceRevisionHash => {
"sourcePath3" => 3,
}
},
},
{
# New test
testName => "two diffs: two non-copies",
diffHashRefsInput => [$diffHashRef1, $diffHashRef2],
expected => {
copyDiffHashRefs => [],
nonCopyDiffHashRefs => [$diffHashRef1, $diffHashRef2],
sourceRevisionHash => {
"indexPath2" => 20,
}
},
},
{
# New test
testName => "two diffs: non-copy and copy",
diffHashRefsInput => [$diffHashRef2, $diffHashRef3],
expected => {
copyDiffHashRefs => [$diffHashRef3],
nonCopyDiffHashRefs => [$diffHashRef2],
sourceRevisionHash => {
"sourcePath3" => 3,
"indexPath2" => 20,
}
},
},
);
my $testCasesCount = @testCases;
plan(tests => $testCasesCount);
foreach my $testCase (@testCases) {
my $testName = $testCase->{testName};
my @diffHashRefs = @{$testCase->{diffHashRefsInput}};
my $expected = $testCase->{expected};
my $got = prepareParsedPatch(0, @diffHashRefs);
is_deeply($got, $expected, $testName);
}
| mogoweb/webkit_for_android5.1 | webkit/Tools/Scripts/webkitperl/VCSUtils_unittest/prepareParsedPatch.pl | Perl | apache-2.0 | 4,137 |
use strict;
use Data::Dumper;
use Carp;
#
# This is a SAS Component
#
=head1 svr_is_hypo [-c N] [-v]
Keep just hypotheticals
------
Example:
svr_all_features 3702.1 peg | svr_is_hypo
would produce a 1-column table containing the hypotheticals in 3702.1
Normally, a stream of feature IDs (PEGs) is used as input. If the things you send
through do not look like PEGs, then they are treated as functional roles.
------
The standard input should be a tab-separated table (i.e., each line
is a tab-separated set of fields). Normally, the last field in each
line would contain the PEG . If some other column contains the PEGs, use
-c N
where N is the column (from 1) that contains the PEG in each case.
This is a pipe command. The input is taken from the standard input, and the
output is to the standard output.
=head2 Command-Line Options
=over 4
=item -c Column
This is used only if the column containing PEGs is not the last.
=item -v [keep only non-hypotheticals]
=back
=head2 Output Format
This is a filter producing a subset of the input lines.
=cut
use SeedUtils;
use SAPserver;
my $sapObject = SAPserver->new();
use Getopt::Long;
my $usage = "usage: svr_is_hypo [-c column] [-v]";
my $column;
my $v;
my $rc = GetOptions('c=i' => \$column,
'v' => \$v);
if (! $rc) { print STDERR $usage; exit }
my @lines = map { chomp; [split(/\t/,$_)] } <STDIN>;
(@lines > 0) || exit;
if (! $column) { $column = @{$lines[0]} }
my @fids = grep { $_ =~ /^fig\|/ } map { $_->[$column-1] } @lines;
my $functions = $sapObject->ids_to_functions(-ids => \@fids);
foreach $_ (@lines)
{
my $thing = $_->[$column-1];
my $func;
if ($thing =~ /^fig\|/)
{
$func = $functions->{$thing};
}
else
{
$func = $thing;
}
my $hypo = &SeedUtils::hypo($func);
if (((! $v) && $hypo) || ($v && (! $hypo)))
{
print join("\t",@$_),"\n";
}
}
| kbase/kb_seed | service-scripts/svr_is_hypo.pl | Perl | mit | 1,901 |
# DE.pm
# by Martin Thurn
# $Id: DE.pm,v 1.0 2003-07-27 21:57:08-04 kingpin Exp kingpin $
=head1 NAME
WWW::Search::AltaVista::DE - class for searching www.AltaVista.DE
=head1 SYNOPSIS
require WWW::Search;
$search = new WWW::Search('AltaVista::DE');
=head1 DESCRIPTION
This class handles making and interpreting AltaVista Germany searches
F<http://www.altavista.de>.
Details of AltaVista can be found at L<WWW::Search::AltaVista>.
This class exports no public interface; all interaction should
be done through WWW::Search objects.
=head1 AUTHOR
Martin Thurn C<mthurn@cpan.org>
=cut
#####################################################################
package WWW::Search::AltaVista::DE;
use WWW::Search::AltaVista;
use strict;
use vars qw( @ISA $VERSION );
@ISA = qw( WWW::Search::AltaVista );
$VERSION = sprintf("%d.%02d", q$Revision: 1.0 $ =~ /(\d+)\.(\d+)/o);
# private
sub native_setup_search
{
my $self = shift;
my $sQuery = shift;
if (!defined($self->{_options})) {
$self->{_options} = {
'nbq' => '50',
'q' => $sQuery,
'search_host' => 'http://de.altavista.com',
'search_path' => '/web/results',
};
};
# Let AltaVista.pm finish up the hard work:
return $self->SUPER::native_setup_search($sQuery, @_);
} # native_setup_search
1;
| carlgao/lenga | images/lenny64-peon/usr/share/perl5/WWW/Search/AltaVista/DE.pm | Perl | mit | 1,465 |
use strict;
use CXGN::Page;
my $page=CXGN::Page->new('chr11b.html','html2pl converter');
$page->header('Chromosome 11');
print<<END_HEREDOC;
<br />
<br />
<center>
<h1><a href="chr11_split.pl">Chromosome 11</a></h1>
<h3>- Section B -</h3>
<br />
<br />
<table summary="">
<tr>
<td align="right" valign="top"><img alt="" align="left"
src="/documents/maps/tomato_arabidopsis/map_images/chr11b.png" border="none" /></td>
</tr>
</table>
</center>
END_HEREDOC
$page->footer(); | solgenomics/sgn | cgi-bin/maps/tomato_arabidopsis/chr11b.pl | Perl | mit | 530 |
package O2CMS::OS::Win32::Process;
# The process handling for win32 system
use strict;
use Win32::Process::Info;
#--------------------------------------------------------------------------------------------
sub new {
my ($package) = @_;
return {}, $package;
}
#--------------------------------------------------------------------------------------------
sub getProcessInformation {
my ($obj, $pid) = @_;
my $pi = Win32::Process::Info->new();
}
#--------------------------------------------------------------------------------------------
sub isAlive {
my ($obj, $pid) = @_;
my $pi = Win32::Process::Info->new();
my %pids = map { $_ => 1 } $pi->ListPids();
return exists $pids{$pid};
}
#--------------------------------------------------------------------------------------------
sub killProcess {
my ($obj, $pid, $exitCode) = @_;
require Win32::Process;
return Win32::Process::KillProcess($pid, $exitCode);
}
#--------------------------------------------------------------------------------------------
1;
| haakonsk/O2-CMS | lib/O2CMS/OS/Win32/Process.pm | Perl | mit | 1,036 |
#!perl -w
use CGI; my $cgi = new CGI;
my $counter = $cgi->param('counter');
if ($counter < 1) { $counter = 1; }
my $next = $counter + 1;
my $url = "simple.pl?counter=$next";
if ($next > 100) {
$url = "frame_done.plex?runs=100";
}
print "Content-Type: text/html\r\n\r\n";
print <<EOF;
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
<HTML>
<HEAD>
<TITLE>PerlEx Performance</TITLE>
<META HTTP-EQUIV="Pragma" CONTENT="no-cache">
<META HTTP-EQUIV="Refresh" CONTENT="0; URL=$url">
</HEAD>
<BODY bgcolor="00ff00">
<font face="verdana, arial, helvetica size="2">
<center>
<H1>
<font size="+9">$counter</font>
<p>
Perl CGI
<p>
</H1>
</center>
</font>
</BODY>
</HTML>
EOF
| amidoimidazol/bio_info | Beginning Perl for Bioinformatics/eg/PerlEx/benchmarks/simple.pl | Perl | mit | 680 |
#!/usr/bin/perl -w
=pod
by Alyx Schubert 6/24/10
This script reads in a file with a list of ID's to find. It returns the data
in the file associated with those ID's.
ARGS: The arguments called to the command line are a list of names/IDs file,
followed by the file to search for them in.
NOTE: It's easiest when both inputted files are sorted and you know that you
will find every ID in the file you are looking for.
NOTE: May need to tailor to whatever kind of file you are parsing through.
Current file type set to: *.ngfa
=cut
my($names, $file, $output, $line1, $line2, $data);
my $ID1 = "NULL";
my $ID2 = "NULL";
my $stat = 0;
my $nomatch = 0;
while(@ARGV)
{
$names = shift(@ARGV);
push(@ARGV, "subset"); #if you want to change the name, change here
$output = join(".", @ARGV);
$file = shift(@ARGV);
shift(@ARGV); #gets rid of the extra name added before
open (NAMES, "<$names") or die ("Cannot open file $names: $!");
open (FILE, "<$file") or die ("Cannot open file $file: $!");
open (OUT, ">>$output") or die ("Cannot open file $output: $!");
while($line1 = <NAMES>)
{
$nomatch = 0;
$stat = 0;
$line1 =~ /^(\S*)/; #nonwhitespace characters
$ID1 = $1;
#print "ID1: $ID1\n";
print OUT ">$ID1\n";
until($ID1 eq $ID2)
{
if(eof(FILE))
{
close (FILE) or die ("Cannot close file $file: $!");
open (FILE, "<$file") or die ("Cannot open file $file: $!");
$stat++;
if($stat>1)
{
print OUT "Match not found\n";
$nomatch = 1;
last;
}
}
$line2 = <FILE>;
$line2 =~ /^>(\S*)/; #nonwhitespace characters followed by tab
$ID2 = $1;
#print "ID2: $ID2\n";
}
if($nomatch == 1)
{
next;
}
$line2 = <FILE>;
$line2 =~ /(\S*)/;
$data = $1;
print OUT "$data\n";
} #end while($line1 = <NAMES>)
close (NAMES) or die ("Cannot close file $names: $!");
close (FILE) or die ("Cannot close file $file: $!");
close (OUT) or die ("Cannot close file $output: $!");
} #end while(@ARGV) | alyxwithay/Personal-Scripts | perl/find_fasta.pl | Perl | mit | 1,993 |
package org::keviny::Database;
use strict;
use warnings;
sub new {
my $class = shift;
my $self = bless {}, $class;
return $self;
}
| kevin-y/learning | perl/logger/org/keviny/Database.pm | Perl | mit | 138 |
/*************************************************************************
name: sensitiveCurt.pl (Volume 1, Chapter 6)
version: April 17, 2001
description: Curt (including consistency and informativity checks)
authors: Patrick Blackburn & Johan Bos
*************************************************************************/
:- module(curt,[curt/0]).
:- ensure_loaded(comsemOperators).
:- use_module(callInference,[callTheoremProver/2,
callModelBuilder/3]).
:- use_module(readLine,[readLine/1]).
:- use_module(comsemPredicates,[memberList/2,
printRepresentations/1]).
:- use_module(kellerStorage,[kellerStorage/2]).
/*========================================================================
Start Curt
========================================================================*/
curt:-
curtTalk([],[],run).
/*========================================================================
Control
========================================================================*/
curtTalk(_,_,quit).
curtTalk(OldReadings,OldModels,run):-
readLine(Input),
curtUpdate(Input,OldReadings-NewReadings,OldModels-NewModels,Moves,State), !,
curtOutput(Moves),
curtTalk(NewReadings,NewModels,State).
/*========================================================================
Curt Help
========================================================================*/
curtHelp:-
nl, write('bye: no more talking'),
nl, write('readings: prints current readings'),
nl, write('models: prints current models'),
nl, write('new: starts a new discourse'),
nl.
/*========================================================================
Curt's output
========================================================================*/
curtOutput([]).
curtOutput([Move|Moves]):-
realizeMove(Move,Output),
format('~n~nCurt: ~p~n',[Output]),
curtOutput(Moves).
/*========================================================================
Curt's Moves
========================================================================*/
realizeMove(clarify,'Want to tell me something?').
realizeMove(bye,'Bye bye!').
realizeMove(accept,'OK.').
realizeMove(contradiction,'No! I do not believe that!').
realizeMove(obvious,'Well, that is obvious!').
realizeMove(noparse,'What?').
/*========================================================================
Update Curt's Information State
========================================================================*/
curtUpdate([],R-R,M-M,[clarify],run):- !.
curtUpdate([bye],R-R,M-M,[bye],quit):- !.
curtUpdate([new],_-[],_-[],[],run):- !.
curtUpdate([help],R-R,M-M,[],run):- !,
curtHelp.
curtUpdate([readings],Readings-Readings,M-M,[],run):- !,
printRepresentations(Readings).
curtUpdate([models],R-R,Models-Models,[],run):- !,
printRepresentations(Models).
curtUpdate(Input,OldReadings-NewReadings,_-Models,Moves,run):-
kellerStorage(Input,Readings), !,
\+ Readings = [],
findall(
Formula,
(
memberList(New,Readings),
(
memberList(Old,OldReadings),
Formula=(New&Old)
;
OldReadings=[],
Formula=New
)
),
UpdatedReadings
),
consistentReadings(UpdatedReadings-NewReadings,Models,TempMoves),
informativeReadings(NewReadings,TempMoves,Moves).
curtUpdate(_,R-R,M-M,[noparse],run).
/*========================================================================
Select Consistent Readings
========================================================================*/
consistentReadings(UpdatedReadings-ConsistentReadings,Models,[Move]):-
findall((Reading,Model),
(
memberList(Reading,UpdatedReadings),
consistent(Reading,Model)
),
Readings),
(
Readings=[],
Move=contradiction
;
\+ Readings=[],
Move=accept
),
findall(R,memberList((R,_),Readings),ConsistentReadings),
findall(M,memberList((_,M),Readings),Models).
/*========================================================================
Consistency Checking calling Theorem Prover and Model Builder
========================================================================*/
consistent(Formula,Model):-
callTheoremProver(~Formula,Proof),
(
Proof=proof, !,
fail
;
DomainSize=20,
callModelBuilder(Formula,DomainSize,Model),
Model=model(_,_)
).
/*========================================================================
Select Informative Readings
========================================================================*/
informativeReadings(Readings,OldMoves,NewMoves):-
\+ memberList((_&_),Readings), !,
NewMoves=OldMoves.
informativeReadings(Readings,OldMoves,NewMoves):-
findall((New&Old),
(
memberList((New&Old),Readings),
informative(Old,New),
Result=informative
),
InformativeReadings),
(
InformativeReadings=[],
NewMoves=[obvious]
;
\+ InformativeReadings=[],
NewMoves=OldMoves
).
/*========================================================================
Informativity Checking calling Theorem Prover and Model Builder
========================================================================*/
informative(Old,New):-
callTheoremProver(~(Old & ~New),Proof),
(
Proof=proof, !,
fail
;
DomainSize=20,
callModelBuilder(Old & ~New,DomainSize,Model),
Model=model(_,_)
).
| TeamSPoon/logicmoo_workspace | packs_sys/logicmoo_nlu/ext/CURT/bb0/sensitiveCurt.pl | Perl | mit | 5,376 |
#!/usr/bin/perl
use strict;
use warnings;
sub quadr_calc
{
my($d,$x,$x1,$x2);
my($a,$b,$c) = @_;
if($a!=0)
{
$d=$b*$b-(4*$a*$c);
if($d<0)
{
print "D<0: No solution";
}
elsif($d==0)
{
$x=(0-$b)/(2*$a);
print "D=0: X1=X2=".$x;
}
elsif($d>0)
{
$x1=((0-$b)+($d**0.5))/(2*$a);
$x2=((0-$b)-($d**0.5))/(2*$a);
print "D>0: X1=".$x1." X2=".$x2;
}
}
else
{
$x=(0-$c)/$b;
print"a=0: Not a qiadratic function! \nX=".$x;
}
}
print "This program takes three numbers (a, b and c) as coefficients\n";
print "of a quadratic equation, calculates its roots, and displays them\n";
print "on the screen for you.\n\n";
print "Please enter the value of a and press <ENTER>: ";
my $a = <STDIN>;
print "\n";
print "Please enter the value of b and press <ENTER>: ";
my $b = <STDIN>;
print "\n";
print "Please enter the value of c and press <ENTER>: ";
my $c = <STDIN>;
print "\n";
quadr_calc($a,$b,$c);
print "\n";
| RadoslavGYordanov/hackerschool | perl/exercise1/exercise1.3.pl | Perl | mit | 932 |
% Most of these operators are native to prolog so we dont have to declare
% them ourselves. The all() and ext() terms takes a unique prolog-level
% variable as its first argument; this variable will not be bound during the
% proof search.
%
:- module(mindi2, [
is_atom/1,
is_literal/1,
tbl_expand/3,
prove/1,
prove/2,
op(200, fx, ~),
op(500, xfy, <=>),
op(500, xfy, =>),
op(520, xfy, &)
]).
:- discontiguous(agent/1).
:- discontiguous(initially/1).
:- discontiguous(initially_known/1).
:- discontiguous(prim_action/1).
:- discontiguous(prim_fluent/1).
:- discontiguous(prim_observation/1).
:- set_prolog_flag(double_quotes, atom).
%:- set_prolog_stack(local, limit(2*10**9)).
:- use_module(library(plunit)).
%:- [utils].
%:- [prover].
%:- [fluent].
%:- [sitcalc].
%:- [domain_party].
%
% utils.pl: some low-level utility predicates.
%
% Copyright 2014, Ryan Kelly
%
% This file supplies some basic low-level utility predicates.
%
%
% ismember(Elem,List) - like member/2, but does not bind variables or
% allow backtracking.
%
ismember(_, []) :- fail.
ismember(E, [H|T]) :-
( E == H ->
true
;
ismember(E, T)
).
%
% findmember(Elem,List,Idx) - like nth0/2, but does not bind variables or
% allow backtracking.
%
findmember(E, L, N) :-
findmember(E, L, 0, N).
findmember(_, [], _, _) :- fail.
findmember(E, [H|T], Acc, N) :-
( E == H ->
N = Acc
;
NextAcc is Acc + 1,
findmember(E, T, NextAcc, N)
).
%
% vdelete(List,Elem,Result) - like delete/3 but using equivalence rather
% than unification, so it can be used on lists
% of variables
%
vdelete([], _, []).
vdelete([H|T], E, Res) :-
( E == H ->
vdelete(T, E, Res)
;
Res = [H|T2],
vdelete(T, E, T2)
).
vdelete_list(L, [], L).
vdelete_list(L, [H|T], L2) :-
vdelete(L, H, L1),
vdelete_list(L1, T, L2).
%
% pairfrom(L,E1,E2,Rest) - E1 and E2 are a pair of (different) elements
% from L, wile Rest is the rest of the list
%
% Like doing (member(E1,L), member(E2,L)) but more efficient, doesn't match
% E1 and E2 to the same element, and doesnt generate equivalent permutations.
%
pairfrom(L, E1, E2, Rest) :-
pairfrom_rec(L, [], E1, E2, Rest).
pairfrom_rec([H|T], Rest1, E1, E2, Rest) :-
E1 = H, select(E2, T, Rest2), append(Rest1, Rest2, Rest)
;
pairfrom_rec(T, [H|Rest1], E1, E2, Rest).
%
% joinlist(+Op,+In,-Out) - join items in a list using given operator
%
joinlist(_, [H], H) :- !.
joinlist(O, [H|T], J) :-
T \= [],
J =.. [O, H, TJ],
joinlist(O, T, TJ).
%
% subs(Name,Value,Old,New) - substitue values in a term
%
% This predicate is true when New is equal to Old with all occurances
% of Name replaced by Value - basically, a symbolic substitution
% routine. For example, it is usually used to produce a result such
% as:
%
% subs(now,S,fluent(now),fluent(S)).
%
subs(X, Y, T, Y) :- T == X, !.
subs(_, _, T, T) :- var(T), !.
subs(X, Y, T, Tr) :-
T =.. [F|Ts],
subs_list(X, Y, Ts, Trs),
Tr =.. [F|Trs].
subs_list(_, _, [], []) :- !.
subs_list(X, Y, [T|Ts], [Tr|Trs]) :-
subs(X, Y, T, Tr),
subs_list(X, Y, Ts, Trs).
:- begin_tests(utils, [sto(rational_trees)]).
test(ismember) :-
ismember(A, [A, B, c]),
ismember(B, [A, B, c]),
ismember(c, [A, B, c]),
\+ ismember(A, [B, _, d]).
test(findmember) :-
findmember(A, [A, B, c], 0),
findmember(B, [A, B, c], 1),
findmember(c, [A, B, c], 2),
\+ findmember(_, [A, B, c], _),
\+ findmember(e, [A, B, c], _).
:- end_tests(utils).
%
% prover.pl: a theorem prover for multi-agent epistemic first-order logic.
%
% Copyright 2008-2014, Ryan Kelly
%
% This is a theorem-prover for the variant of modal logic used in our
% fluent domain, based on the ideas in leanTAP [1] and its expansion to
% modal logic by Fitting [2]. It's a classic tableaux-style prover that
% tries to refute a formula by closing all branches of its tableaux, and
% it handles modalities by building an auxiliary tableaux for each new
% modal world until it finds one that can be closed.
%
% [1] Bernhard Beckert and Joachim Posegga.
% leanTAP: Lean tableau-based deduction.
% Journal of Automated Reasoning, 15(3):339-358, 1995.
%
% [2] Melvin Fitting.
% leanTAP Revisited
% Journal of Logic and Computation, 8(1):33-47, 1998.
%
% It is, sadly, a lot less "lean" than the source material due to several
% additions that make it more suitable for use with situation calculus
% domains:
%
% * Support for an distinct set of "axioms" which are known to hold
% at all worlds in the model, to represent the background theory
% of the domain.
%
% * Special-case handling of term equality, assuming rigid terms and
% unique-names axioms.
%
% * Use of attributed variables to track each free variable back to
% its source formula, and avoid making multiple instanciations of
% the formula with the some variable bindings.
%
% * More care taken to try to terminate when the tableaux cannot be
% closed, since calculation of the persistence condition requires
% a terminating decision procedure.
%
% Our logical terms and operators are:
%
% true - truth literal (ie "top")
% false - falsehood literal (ie "bottom")
% p(...) - predicate, optionally with term arguments
% A = B - term equality
% ~P - negation
% P & Q - logical and
% P | Q - logical or
% P => Q - implication
% P <=> Q - equivalence
% all([Xs], P) - universal quantification (positive scope only)
% ~ext([Xs], P) - existential quantification (negative scope only)
% knows(A,P) - agent knowledge modality
%
% There is no support for existential quantification, this must be handled
% handled in a pre-processing step. Our treatment of equality-as-unification
% means skolemization is not possible, so for now, existential quantifiers
% will have to be expanded out into a finite disjunction of possibilities.
%
%
% is_atom(P) - the formula P is a literal atom, not a compound expression
% is_literal(P) - the formula P is a literal atom or the negation of one
%
% This can be used to detect the base case of predicates that structurally
% decompose formulae.
%
is_atom(P) :-
P \= (~_),
P \= (_ => _),
P \= (_ <=> _),
P \= (_ & _),
P \= (_ | _),
P \= ext(_, _),
P \= all(_, _),
P \= knows(_, _).
is_literal(~P) :- !, is_atom(P).
is_literal(P) :- is_atom(P).
%
% prove/1 and prove/2: top-level driver for the prover.
%
% These predicates attempt to prove a formula by refuting its negation.
% The optional set of axioms are formulae known to hold at all worlds
% reachable in the model. This list must not include any modalities,
% or the prover may get stuck in a loop expanding copies of the same
% modality over and over.
%
prove(Fml) :-
prove([], Fml).
prove(Axioms, Fml) :-
prove_iterdeep(Axioms, Fml, 500).
prove_iterdeep(Axioms, Fml, Limit) :-
% Classic iterative-deepening for completeness, for which
% swi-prolog conveniently provides builtin support via the
% call_with_depth_limit/3 predicate.
refute_with_depth_limit(Axioms, ~Fml, Limit, Result),
( Result = depth_limit_exceeded ->
%write(not_proved_at_depth(Limit)), nl,
NewLimit is Limit + 500,
prove_iterdeep(Axioms, Fml, NewLimit)
;
%write(proved_at_depth(Result)), nl
true
).
refute_with_depth_limit(Axioms, Fml, Limit, Result) :-
tbl_init(Axioms, Tbl),
call_with_depth_limit(refute(Fml, Tbl), Limit, Result).
refute(Fml, Tbl) :-
% Try to expand the given tableaux with the given formula so that
% all branches are closed. Since tbl_expand/3 generates all 'closed'
% solutions before generating any 'open' solutions, we can safely
% cut after the first solution and avoid lots of pointless backtracking.
tbl_expand(Fml, Tbl, Res),
!, Res=closed(_).
%
% tbl_expand/3: build a fully-expanded tableaux from the given state.
%
% This is the core of the prover. In the style of leanTaP, it takes the
% current state of an under-construction tableaux and tries to expand it
% into one where all branches are closed. Unlike leanTaP, we use an explicit
% "tableaux state" data structure to pass around the state, since our version
% contains quite a few more auxiliary fields.
%
% The state of the tableaux branch at each invocation represents a partially-
% built model based at a particular world of the underlying kripke structure.
%
% The expansion proceeds by expanding all formulae on the branch, trying
% to produce a conflicting pair of literals at the current world that will
% close the branch. If this is not possible then one of the related worlds
% implied by the model is selected and the search continues in a sub-tableaux
% at that world.
%
% If all branches are successfully closed, the predicate's third argument
% will be bound to 'closed(NEqs)' where NEqs is a possibly-empty list of
% pairs of terms that must not unify. If some branch remains open then
% its third argument will be bound to the atom 'open'.
%
% All 'closed' solutions will be generated before any 'open' solutions.
%
% Normalization rules.
% These decompose higher-level connectives into simpler ones by
% e.g. pushing negation inside other operators. This effectively
% computes the required normal form at runtime.
tbl_expand(~(~X), Tbl, Res) :-
!, tbl_expand(X, Tbl, Res).
tbl_expand(X => Y, Tbl, Res) :-
!, tbl_expand((~X) | Y, Tbl, Res).
tbl_expand(X <=> Y, Tbl, Res) :-
!, tbl_expand((X & Y) | (~X & ~Y), Tbl, Res).
tbl_expand(~(X & Y), Tbl, Res) :-
!, tbl_expand((~X) | (~Y), Tbl, Res).
tbl_expand(~(X | Y), Tbl, Res) :-
!, tbl_expand(~X & ~Y, Tbl, Res).
tbl_expand(~(X => Y), Tbl, Res) :-
!, tbl_expand(X & (~Y), Tbl, Res).
tbl_expand(~(X <=> Y), Tbl, Res) :-
!, tbl_expand(((~X) | (~Y)) & (X | Y), Tbl, Res).
tbl_expand(~ext(Vs, P), Tbl, Res) :-
!, tbl_expand(all(Vs, ~P), Tbl, Res).
% Rule to handle universal quantification.
% We create a new instance of the quantified formula using a fresh
% variable, and stash the original formula in the tableaux state for
% future re-use. It will only be re-used if the previous instance of
% that formula is bound during the search, to ensure that we don't keep
% pointlessly re-using the same formula over and over.
tbl_expand(all([], P), Tbl, Res) :-
!,
tbl_expand(P, Tbl, Res).
tbl_expand(all([X|Xs], P), Tbl, Res) :-
!,
tbl_add_univ_fml(Tbl, all(X, all(Xs, P)), InstFml, Tbl2),
tbl_expand(InstFml, Tbl2, Res).
% Rule to guard against existential quantification.
% Existential quantification is not supported, and must be handled as a
% pre-processing step before passing formulae to the prover. This rule
% proides a simple sanity-check.
tbl_expand(ext(_, _), _, _) :-
!, write(formula_cannot_contain_existential_quantifiers), nl, fail.
tbl_expand(~all(_, _), _, _) :-
!, write(formula_cannot_contain_existential_quantifiers), nl, fail.
% Rules for collecting modalities.
% Modalities don't constrain the current world, but rather the worlds
% that may be reachable from the current one. They are simply collected
% along the branch and used to imply/constraint other worlds that we might
% move to if the current one cannot be closed.
tbl_expand(knows(A, F), Tbl, Res) :-
!,
tbl_add_necc(Tbl, k(A, F), Tbl2),
tbl_expand(true, Tbl2, Res).
tbl_expand(~knows(A, F), Tbl, Res) :-
!,
tbl_add_poss(Tbl, k(A, ~F), Tbl2),
tbl_expand(true, Tbl2, Res).
% Rule for handling disjunction.
% The tableaux bifurcates and we must try to close both branches, ensuring
% that any declared non-unifiability of terms is respected across both
% branches.
%
% Note that our use of prolog variables when instantiating universally-
% quantified formulae means that free-variable substitutions apply across
% both branches, as required for a first-order tableaux.
tbl_expand(X | Y, Tbl, Res) :-
!,
% First try to close the LHS branch.
tbl_expand(X, Tbl, ResX),
( ResX = closed(NEqsX) ->
% Ensure that the RHS proof search doesn't unify things that the LHS
% proof search declared must not unify.
tbl_add_neqs(Tbl, NEqsX, Tbl2),
tbl_expand(Y, Tbl2, ResY),
( ResY = closed(NEqsY) ->
% Combine the things-that-must-not-unify lists from both branches.
append(NEqsX, NEqsY, NEqs),
Res = closed(NEqs)
;
% The RHS could not be closed.
% Backtrack to a different solution for the LHS.
fail
)
;
% The LHS could not be closed, so the whole tableaux stays open.
Res = open
).
% Rule for handling conjunction.
% Both sides simply get added to the existing branch.
tbl_expand(X & Y, Tbl, Res) :-
!,
tbl_push_fml(Tbl, Y, Tbl2),
tbl_expand(X, Tbl2, Res).
% Rule for closing the branch, or continuing the search.
%
% The formula under consideration here must be a (possibly negated)
% literal, since any other form would have matched a rule above.
%
% We add the literal to the current tableaux state. If that produces a
% contradiction then we're done on this branch. If not then the tableaux
% remains open and we proceed as follows:
%
% * If we have more unexpanded formulae on the branch, continue
% expanding the current branch.
%
% * If we have universal formulae where all instances have been used,
% add fresh instances of them to the unexpanded list and continue
% expanding the current branch.
%
% * Enumerate the alternative worlds implied by the current tableaux
% state, expanding a sub-tableaux for each:
%
% * If any such sub-tableaux is closed, close the current branch.
%
% * If all sub-tableaux remain open, check again for universal
% formulae where all instances have been used. If we have any
% then add fresh instances of them to the unexpanded list and
% resume expanding the current branch.
%
% * Otherwise, there is no way to close the current branch, so report
% it as being open.
%
% This rather heavy-handled imperative control flow is designed to avoid
% repeatedly instantiating the same universally-quantified formula over
% and over, without stopping the search too early. It has been found to
% help termination in cases that obviously cannot be expanded to a closed
% state, but for which a naive handling of universally-quantified formulae
% would recurse forever.
%
tbl_expand(Lit, Tbl, Res) :-
(
tbl_add_literal(Tbl, Lit, Tbl2),
( Tbl2 = closed(NEqs) ->
Res = closed(NEqs)
;
( tbl_pop_fml(Tbl2, Fml, Tbl3) ->
tbl_expand(Fml, Tbl3, Res)
;
tbl_copy_used_univ_fmls(Tbl2, Tbl3),
( tbl_pop_fml(Tbl3, Fml, _S_Tbl4a) ->
tbl_expand(Fml, Tbl3, Res)
;
tbl_expand_subtbls(Tbl2, SubRes),
( SubRes = closed(NEqs) ->
Res = closed(NEqs)
;
tbl_copy_used_univ_fmls(Tbl2, Tbl3),
( tbl_pop_fml(Tbl3, Fml, _S_Tbl4b) ->
tbl_expand(Fml, Tbl3, Res)
;
Res = open
)
)
)
)
)
;
% After all other possibilities have been exhaused, we want to make
% sure to generate an 'open' solution so that failure-driven backtracking
% will work correctly.
Res = open
).
% Helper predicate for expanding each sub-tableaux in turn.
% This enumerates all the possible sub-tableaux and then walks the
% list trying to close them. It will unify its second argument with
% 'closed' if one of the sub-tableaux could be closed, and with 'open'
% if they all remain open.
%
% Like tbl_expand/3 this will backtrack over different possible ways
% to close each sub-tableaux.
tbl_expand_subtbls(Tbl, Res) :-
findall(SubTbl, tbl_pick_subtbl(Tbl, SubTbl), SubTbls),
tbl_expand_subtbls(Tbl, SubTbls, Res).
tbl_expand_subtbls(_, [], open).
tbl_expand_subtbls(Tbl, [SubTbl | SubTbls], Res) :-
tbl_expand(true, SubTbl, SubRes),
( SubRes = closed(NEqs) ->
Res = closed(NEqs)
;
tbl_expand_subtbls(Tbl, SubTbls, Res)
).
%
% tbl_* - utility predicates for maintaining in-progess tableaux state.
%
% The following are low-level state manipulation routines for the tableaux.
% They're mostly just list-shuffling and could have been done inline in the
% spirit of leanTaP, but factoring them out helps the code read better and
% leaves the door open for e.g. better data structures.
%
% The full state of a tableaux branch is a term:
%
% tbl(UnExp, TLits, FLits, NEqs, Axs, Necc, Poss, Univ, FVs)
%
% Its arguments are:
%
% * UnExp: a list of formulae remaining to be expanded on the branch.
% * TLits: a list of literals true at the current world.
% * FLits: a list of literals false at the current world.
% * NEqs: a list of A=B pairs that are not allowed to unify.
% * Axs: a list of formulae true at every possible world.
% * Necc: a list of formulae that hold at all accessible worlds,
% indexed by name of accessibility relation
% * Poss: a list of formulae that hold at some accessible world,
% indexed by name of accessibility relation
% * Univ: a list of universally-quantified formulae that can be used
% on the branch, along with previous instantiation variables.
% * FVs: a list of free variables instantiated by the prover, which
% must be preserved when copying formulae.
%
%
% tbl_init/2 - initialize a new empty tableaux
%
% This predicate takes a list of axioms that are true at every world,
% and produces an initialized tableux state.
%
tbl_init(Axs, TblOut) :-
TblOut = tbl(Axs, [], [], [], Axs, [], [], [], []).
tbl_write(Tbl) :-
Tbl = tbl(UE, TLits, FLits, NEqs, _, Necc, Poss, Univ, _),
write(tbl), nl,
write(' UE = '), write(UE), nl,
write(' TLits = '), write(TLits), nl,
write(' FLits = '), write(FLits), nl,
write(' NEqs = '), write(NEqs), nl,
write(' Necc = '), write(Necc), nl,
write(' Poss = '), write(Poss), nl,
tbl_write_univ(Univ).
tbl_write_univ([]).
tbl_write_univ([U|Univ]) :-
write(' Univ: '), write(U), nl,
tbl_write_univ(Univ).
%
% tbl_push_fml/3 - add a formula to be expanded on this tableaux branch
% tbl_pop_fml/3 - pop a formula off the unexpanded list for this branch
%
% These predicates simply push/push from a list of yet-to-be-expanded
% formulae, basically maintaining a worklist for the current branch.
%
tbl_push_fml(TblIn, Fml, TblOut) :-
TblIn = tbl(UE, TLits, FLits, NEqs, Axs, Necc, Poss, Univ, FVs),
TblOut = tbl([Fml|UE], TLits, FLits, NEqs, Axs, Necc, Poss, Univ, FVs).
tbl_pop_fml(TblIn, Fml, TblOut) :-
TblIn = tbl([Fml|UE], TLits, FLits, NEqs, Axs, Necc, Poss, Univ, FVs),
TblOut = tbl(UE, TLits, FLits, NEqs, Axs, Necc, Poss, Univ, FVs).
%
% tbl_add_neqs/3 - add non-unification constraints to the tableaux
%
% This predicate declares that the list of [A=B] pairs in its second arugment
% must not be made to unify, recording them in an internal list in the
% tableaux state. Subsequent attempts to bind free variables will be
% checked for compatability with this list.
%
tbl_add_neqs(TblIn, NEqs, TblOut) :-
TblIn = tbl(UnExp, TLits, FLits, NEqsIn, Axs, Necc, Poss, Univ, FVs),
append(NEqs, NEqsIn, NEqsOut),
TblOut = tbl(UnExp, TLits, FLits, NEqsOut, Axs, Necc, Poss, Univ, FVs).
%
% tbl_add_necc/4 - add a formula that holds at all possible worlds
% tbl_add_poss/4 - add a formula that holds at some possible world
%
% These predicates are used to accumulate information about worlds reachable
% from the current one. This information is then used to initialize a
% sub-tableuax if the proof moves to a new world.
%
tbl_add_necc(TblIn, N, TblOut) :-
TblIn = tbl(UnExp, TLits, FLits, NEqs, Axs, Necc, Poss, Univ, FVs),
TblOut = tbl(UnExp, TLits, FLits, NEqs, Axs, [N|Necc], Poss, Univ, FVs).
tbl_add_poss(TblIn, P, TblOut) :-
TblIn = tbl(UnExp, TLits, FLits, NEqs, Axs, Necc, Poss, Univ, FVs),
TblOut = tbl(UnExp, TLits, FLits, NEqs, Axs, Necc, [P|Poss], Univ, FVs).
%
% tbl_add_univ_fml/4 - add a universally-quantified formula to the tableaux
%
% This predicate is applied to universally-quantified formula found during
% the expansion. It produces an instance of the formula with a fresh variable
% and notes the formula for potential re-use in the future.
%
tbl_add_univ_fml(TblIn, all(X, P), InstFml, TblOut) :-
TblIn = tbl(UnExp, TLits, FLits, NEqs, Axs, Necc, Poss, Univ, FVs),
tbl_copy_term(TblIn, [X, P], [V, InstFml]),
% Remember where this var come from, so we can avoid duplicate bindings.
put_attr(V, mindi2, []),
U = u(X, P, [V]),
TblOut = tbl(UnExp, TLits, FLits, NEqs, Axs, Necc, Poss, [U|Univ], [V|FVs]).
%
% tbl_copy_term/2 - copy term while preserving unbound vars.
%
% This predicate can be used like copy_term/2 expect that it will not
% rename unbound free variables in the formula. Basically it renames
% variables defined outside of the proof search, while maintaining any
% variables created by the search itself.
%
tbl_copy_term(Tbl, TermIn, TermOut) :-
Tbl = tbl(_, _, _, _, _, _, _, _, FVs),
copy_term([TermIn, FVs], [TermOut, FVs]).
%
% tbl_copy_used_univ_fmls/2 - make fresh copes of used universal formulae
%
% This predicate finds any universally-quantified formula for which all
% existing instances have been "used" - that is, have had their instance
% variable bound. If it finds any then it copies fresh instances of them
% into the list of unexpanded formulae.
%
% This is a simple way to avoid making lots of useless duplicate expansions
% of universally-quantified formulae.
%
tbl_copy_used_univ_fmls(TblIn, TblOut) :-
TblIn = tbl([], TLits, FLits, NEqs, Axs, Necc, Poss, UnivIn, FVs),
TblOut = tbl(UnExp, TLits, FLits, NEqs, Axs, Necc, Poss, UnivOut, FVs),
tbl_copy_used_univ_fmls_rec(TblIn, UnivIn, UnivOut, UnExp).
tbl_copy_used_univ_fmls_rec(_, [], [], []).
tbl_copy_used_univ_fmls_rec(Tbl, [U|UnivIn], UnivOut, UnExp) :-
U = u(X, P, Vars),
Vars = [PrevV|_],
( ( \+ var(PrevV) ) ->
tbl_copy_term(Tbl, [X, P], [NewV, NewP]),
% Remember where this var come from, so we can avoid duplicate bindings.
put_attr(NewV, mindi2, Vars),
UnivOut = [u(X, P, [NewV|Vars])|UnivOutRest],
UnExp = [NewP|UnExpRest]
;
UnivOut = [U|UnivOutRest],
UnExp = UnExpRest
),
tbl_copy_used_univ_fmls_rec(Tbl, UnivIn, UnivOutRest, UnExpRest).
%
% tbl_pick_subtbl/2 - generate a sub-tableaux for a related world
%
% The tableaux state contains a collection of "possible" and "necessary"
% formulae that imply the existence of other worlds related to the one
% currently under consideration. This predicate picks one such world
% and returns a new tableaux based on the formulae relevant to that world8,
% backtracking over each choice in turn.
%
tbl_pick_subtbl(Tbl, SubTbl) :-
Tbl = tbl(_, _, _, NEqs, Axioms, Necc, Poss, _, FVs),
% Pick a possible world.
member(k(A, F), Poss),
% Pair it with all the things that necessarily hold there.
( bagof(FN, member(k(A, FN), Necc), FNs) ->
copy_term(Axioms, AXs),
append(FNs, AXs, FNecc)
;
copy_term(Axioms, FNecc)
),
SubTbl = tbl([F|FNecc], [], [], NEqs, Axioms, [], [], [], FVs).
tbl_pick_subtbl(Tbl, SubTbl) :-
Tbl = tbl(_, _, _, NEqs, Axioms, Necc, Poss, _, FVs),
% Pick an agent for whom no possible world was implied.
% We assume that they consider at least one world possible,
% so we can check the consistency of their knowledge.
setof(A, F^(member(k(A, F), Necc), \+ member(k(A, _), Poss)), AllA),
member(A, AllA),
% Pair it with all the things that necessarily hold there.
( bagof(FN, member(k(A, FN), Necc), FNs) ->
copy_term(Axioms, AXs),
append(FNs, AXs, FNecc)
;
copy_term(Axioms, FNecc)
),
SubTbl = tbl(FNecc, [], [], NEqs, Axioms, [], [], [], FVs).
%
% tbl_add_literal/3 - expand the branch with a new literal
%
% This predicate attempts to add a new literal to the branch.
%
% It first tries to add it in such a way as to form a contradiction, in
% which case the third argument is bound to closed(NEqs) with NEqs a list
% of A=B pairs that must *not* be made to unify on some other branch.
%
% If closing the branch fails, it adds the literal to the appropriate field
% in the tableaux state and binds the third argument to the new tableaux.
%
% This is really the heart of the prover, where the contrdictions are made.
% It has special-case handling of equality based on rigid terms and unique
% names axioms, meaning we can treat it using unification.
%
tbl_add_literal(Tbl, true, Tbl) :- !.
tbl_add_literal(Tbl, ~false, Tbl) :- !.
tbl_add_literal(_, false, closed([])) :- !.
tbl_add_literal(_, ~true, closed([])) :- !.
tbl_add_literal(TblIn, A=B, TblOut) :-
!,
( unifiable(A, B, Bindings) ->
( Bindings = [] ->
% The terms are identical, so this literal is a tautology.
TblOut = TblIn
;
(
% This can be made into a contradiction by insisting that any one of
% the free-variable bindings be in fact un-unifiable.
member(Binding, Bindings),
TblOut = closed([Binding])
;
% Or the branch can be left open, and we just do the bindings.
tbl_apply_var_bindings(TblIn, Bindings, TblOut)
)
)
;
% The terms are not unifiable, so this literal is a contradiction.
TblOut = closed([])
).
tbl_add_literal(TblIn, ~(A=B), TblOut) :-
!,
( unifiable(A, B, Bindings) ->
( Bindings = [] ->
% The terms are identical, so this literal is a contradiction.
TblOut = closed([])
;
(
% This literal can be made into a contradiction via unification.
tbl_apply_var_bindings(TblIn, Bindings),
TblOut = closed([])
;
% Or the branch can be left open by not doing the bindings.
tbl_add_neqs(TblIn, [A=B], TblOut)
)
)
;
% The terms are not unifiable, so this literal is a tautology.
TblOut = TblIn
).
tbl_add_literal(TblIn, ~Lit, TblOut) :-
!,
TblIn = tbl(UnExp, TLits, FLitsIn, NEqs, Axs, Necc, Poss, Univ, FVs),
% Try to produce a contradiction with one of the true literals.
tbl_add_literal_find_contradiction(TblIn, Lit, TLits, Res),
( Res = closed ->
TblOut = closed([])
;
% Add it to the list of things known to be false, unless we already know.
( ismember(Lit, FLitsIn) ->
FLitsOut = FLitsIn
;
FLitsOut = [Lit|FLitsIn]
),
TblOut = tbl(UnExp, TLits, FLitsOut, NEqs, Axs, Necc, Poss, Univ, FVs)
).
tbl_add_literal(TblIn, Lit, TblOut) :-
!,
TblIn = tbl(UnExp, TLitsIn, FLits, NEqs, Axs, Necc, Poss, Univ, FVs),
% Try to produce a contradiction with one of the false literals.
tbl_add_literal_find_contradiction(TblIn, Lit, FLits, Res),
( Res = closed ->
TblOut = closed([])
;
% Add it to the list of things known to be true, unless we already know.
( ismember(Lit, TLitsIn) ->
TLitsOut = TLitsIn
;
TLitsOut = [Lit|TLitsIn]
),
TblOut = tbl(UnExp, TLitsOut, FLits, NEqs, Axs, Necc, Poss, Univ, FVs)
).
%
% Helper predicate to search for contradictions in a set of complimentary
% literals. It first tries to find a member identical to the target,
% in which case the branch is always closed and no backtracking is required.
% Otherwise, it tries to find one unifiable with the taret, but allows
% backtracking over these choices. If all such choices are backtracked over
% (or none are found) then the branch remains open.
%
tbl_add_literal_find_contradiction(Tbl, Lit, NLits, Res) :-
tbl_add_literal_find_contradiction_bindings(Lit, NLits, Bindings),
( Bindings = [] ->
% No possible bindings, so we fail to find any contraditions.
Res = open
;
sort(Bindings, OrderedBindings),
( OrderedBindings = [[]|_] ->
% Found a contradiction with no bindings, so no need to backtrack.
Res = closed
;
% Found a contradiction if we do some backtrackable unification.
(
member(B, OrderedBindings),
tbl_apply_var_bindings(Tbl, B),
Res = closed
;
Res = open
)
)
).
tbl_add_literal_find_contradiction_bindings(_, [], []).
tbl_add_literal_find_contradiction_bindings(Lit, [NLit|NLits], Bindings) :-
( unifiable(Lit, NLit, B) ->
Bindings = [B|Bs],
tbl_add_literal_find_contradiction_bindings(Lit, NLits, Bs)
;
tbl_add_literal_find_contradiction_bindings(Lit, NLits, Bindings)
).
%
% tbl_apply_var_bindings/2
% tbl_apply_var_bindings/3 - apply variable bindings and check constraints
%
% This predicate takes a list of [A=B] pairs makes them unify with occurs
% check. It also checks that various proof-search constraints are not
% violated by the bindings:
%
% * two free variables generated from the same source formula are never
% bound to an identical term, as this would be redundant.
%
% * any declared non-unifiability constrains are not violated.
%
% If called with three arguments, this predicate will also remove any
% non-unifiability constraints that have become tautological and return
% the updated tableaux state in its third argument.
%
tbl_apply_var_bindings(TblIn, Bindings) :-
tbl_apply_var_bindings(TblIn, Bindings, _).
tbl_apply_var_bindings(TblIn, [], TblOut) :-
tbl_check_neqs(TblIn, TblOut).
tbl_apply_var_bindings(TblIn, [A=B|Bindings], TblOut) :-
unify_with_occurs_check(A, B),
tbl_apply_var_bindings(TblIn, Bindings, TblOut).
attr_unify_hook(OtherValues, Value) :-
% This hook gets called when one of our free variables is bound.
% Veto the binding if it is bound to a previously-used value, since
% that's redundant for the proof search.
\+ ismember(Value, OtherValues).
%
% Helper predicate to check that non-unifiability constraints have
% not been violated. It also helps to trim down the list of constraints
% if some have become tautological.
%
tbl_check_neqs(TblIn, TblOut) :-
TblIn = tbl(UnExp, TLits, FLits, NEqsIn, Axs, Necc, Poss, Univ, FVs),
tbl_check_neqs_list(NEqsIn, NEqsOut),
TblOut = tbl(UnExp, TLits, FLits, NEqsOut, Axs, Necc, Poss, Univ, FVs).
tbl_check_neqs_list([], []).
tbl_check_neqs_list([A=B|NEqsIn], NEqsOut) :-
( unifiable(A, B, Bindings) ->
Bindings \= [],
NEqsOut = [A=B|NEqsOutRest],
tbl_check_neqs_list(NEqsIn, NEqsOutRest)
;
tbl_check_neqs_list(NEqsIn, NEqsOut)
).
%
% Test cases for basic prover functionality.
%
:- begin_tests(prover, [sto(rational_trees)]).
test(prop1) :-
prove(true),
prove(~false),
prove(red = red),
prove(~(red = blue)),
prove(p | ~p),
\+ prove(p | q).
test(prop2) :-
prove([q], p | q).
test(knows1) :-
prove(knows(ann, p | ~p)),
\+ prove(knows(ann, p | q)),
\+ prove(knows(ann, p & ~p)).
test(knows2) :-
prove([q], knows(ann, p | q)).
test(knows4) :-
prove(knows(ann, knows(bob, p)) => knows(ann, knows(bob, p | q))),
\+ prove(knows(ann, knows(bob, p | q)) => knows(ann, knows(bob, p))).
test(knows5) :-
prove([(p | q)], knows(ann, knows(bob, p | q))).
test(knows6) :-
prove(knows(ann, knows(bob, p(c) | ~p(c)))).
test(knows7) :-
prove(knows(ann, p(c)) => knows(ann, ext([X], p(X)))),
prove(knows(ann, all([X], p(X))) => knows(ann, p(c))).
test(knows12) :-
prove(knows(ann, knows(bob, p(x))) => ext([X], knows(ann, knows(bob, p(X))))),
prove(knows(ann, knows(bob, p(x))) => knows(ann, ext([X], knows(bob, p(X))))),
prove(knows(ann, knows(bob, p(x))) => knows(ann, knows(bob, ext([X], p(X))))).
test(eq1) :-
prove(all([X], (X=red) => hot(X)) => hot(red)).
:- end_tests(prover).
%
% fluent.pl: predicates for manipulating fluent terms
%
% Copyright 2008-2014, Ryan Kelly
%
% This file supplies some basic predicates for manipulating and reasoning
% about reified fluent terms. It relies on prover.pl for the core reasoning
% engine.
%
% Variables are expected to be actual prolog variables, as this vastly
% increases the simplicity and efficiency of certain operations. It also
% means we need to take extra care in some other areas. In particular,
% we assume that the formula contains the *only* references to those
% variables, so we are free to bind them in simplification and reasoning.
%
%
% normalize(F,N) - perform some basic normalisations on a formula
%
% This is designed to make formulae easier to reason about. It
% re-arranges orderless terms into a standard order, for example
% the arguments to '=' and the list of variables in a quantification.
% It also simplifies away some trivial tautologies.
%
normalize((A=B), (A=B)) :-
A @< B, !.
normalize((A=B), (B=A)) :-
B @< A, !.
normalize((A=B), true) :-
A == B, !.
normalize(ext(X, P), ext(Y, Q)) :-
sort(X, Y),
normalize(P, Q), !.
normalize(all(X, P), all(Y, Q)) :-
sort(X, Y),
normalize(P, Q), !.
normalize(~P, ~Q) :-
normalize(P, Q), !.
normalize((P1 & Q1), (P2 & Q2)) :-
normalize(P1, P2),
normalize(Q1, Q2), !.
normalize((P1 | Q1), (P2 | Q2)) :-
normalize(P1, P2),
normalize(Q1, Q2), !.
normalize((P1 => Q1), (P2 => Q2)) :-
normalize(P1, P2),
normalize(Q1, Q2), !.
normalize((P1 <=> Q1), (P2 <=> Q2)) :-
normalize(P1, P2),
normalize(Q1, Q2), !.
normalize(knows(A, P), knows(A, Q)) :-
normalize(P, Q), !.
normalize(P, P).
%
% struct_equiv(P, Q) - two formulae are structurally equivalent,
% basically meaning they are identical up
% to renaming of variables.
%
% struct_oppos(P, Q) - two formulae are structurally opposed,
% making their conjunction a trivial falsehood.
%
struct_equiv(P, Q) :-
is_atom(P), is_atom(Q), P == Q.
struct_equiv(P1 & P2, Q1 & Q2) :-
struct_equiv(P1, Q1),
struct_equiv(P2, Q2).
struct_equiv(P1 | P2, Q1 | Q2) :-
struct_equiv(P1, Q1),
struct_equiv(P2, Q2).
struct_equiv(P1 => P2, Q1 => Q2) :-
struct_equiv(P1, Q1),
struct_equiv(P2, Q2).
struct_equiv(P1 <=> P2, Q1 <=> Q2) :-
struct_equiv(P1, Q1),
struct_equiv(P2, Q2).
struct_equiv(~P, ~Q) :-
struct_equiv(P, Q).
struct_equiv(ext([], P), ext([], Q)) :-
struct_equiv(P,Q).
struct_equiv(ext([V1|Vs1], P), ext([V2|Vs2], Q)) :-
subs(V1, V2, P, P1),
struct_equiv(ext(Vs1, P1), ext(Vs2, Q)).
struct_equiv(all([], P), all([], Q)) :-
struct_equiv(P, Q).
struct_equiv(all([V1|Vs1], P), all([V2|Vs2], Q)) :-
subs(V1, V2, P, P1),
struct_equiv(all(Vs1, P1), all(Vs2, Q)).
struct_equiv(knows(A, P), knows(A, Q)) :-
struct_equiv(P, Q).
struct_oppos(P, Q) :-
P = ~P1, struct_equiv(P1, Q) -> true
;
Q = ~Q1, struct_equiv(P, Q1) -> true
;
P=true, Q=false -> true
;
P=false, Q=true.
%
% fml_compare - provide a standard order over formula terms
%
% This allows them to be sorted, have duplicates removed, etc.
% Formula should be normalised before this is applied.
%
fml_compare('=', F1, F2) :-
struct_equiv(F1, F2), !.
fml_compare(Ord, F1, F2) :-
( F1 @< F2 ->
Ord = '<'
;
Ord = '>'
).
%
% contains_var(A, V) - formula A contains variable V
%
% ncontains_var(A, V) - formula A does not contain variable V
%
%
% Since we know that V is a variable, we do this test by making a copy,
% grounding the copied variable, then checking for structural equivalence
% with the original term.
%
contains_var(A,V) :-
copy_term(A:V,A2:V2),
V2=groundme,
A \=@= A2.
ncontains_var(A,V) :-
copy_term(A:V,A2:V2),
V2=groundme,
A =@= A2.
%
% flatten_op(Op, Terms, Result) - flatten repeated ops into a list
%
% This predicate succeeds when Result is a list of terms from Terms,
% which were joined by the operator Op. It basically allows a tree of
% similar operators such as ((A & B) & (C & (D & E))) to be flattened
% into a list (A,B,C,D,E).
%
flatten_op(_, [], []).
flatten_op(O, [T|Ts], Res) :-
( T =.. [O|Args] ->
append(Args, Ts, Ts2),
flatten_op(O, Ts2, Res)
;
Res = [T|Res2],
flatten_op(O, Ts, Res2)
).
%
% flatten_quant(Q, Ts, VarsIn, VarsOut, Body) - flatten nested quantifiers
%
flatten_quant(Q, T, Acc, Vars, Body) :-
( T =.. [Q, Vs, T2] ->
append(Vs, Acc, Acc2),
flatten_quant(Q, T2, Acc2, Vars, Body)
;
Vars = Acc,
Body = T
).
%
% flatten_quant_and_simp(Q, BodyIn, VarsIn, VarsOut, BodyOut)
% - flatten nested quantifiers, and apply simplification
%
% Just like flatten_quant/5 above, but applies simplify/2 to the body
% when it does not match the quantifier, in case its simplification
% does match.
%
flatten_quant_and_simp(Q, T, VarsIn, VarsOut, Body) :-
( T =.. [Q, V, T2] ->
append(V, VarsIn, Vars2),
flatten_quant_and_simp(Q, T2, Vars2, VarsOut, Body)
;
simplify1(T, Tsimp),
( Tsimp =.. [Q, V, T2] ->
append(V, VarsIn, Vars2),
flatten_quant_and_simp(Q, T2, Vars2, VarsOut, Body)
;
Body = Tsimp, VarsIn = VarsOut
)
).
%
% indep_of_vars(Vars, P) - P contains none of the vars in the list Vars,
% i.e. it is independent of the vars.
%
indep_of_vars(Vars, P) :-
\+ ( member(X, Vars), contains_var(P, X) ).
%
% simplify(+F1, -F2) - simplify a formula
%
% This predicate applies some basic simplification rules to a formula
% to eliminate redundancy and (hopefully) speed up future reasoning.
% This can be particularly important when applying regression, which
% tends to result in a large increase in formula size.
%
simplify(P, S) :-
normalize(P, Nml),
simplify1(Nml, S), !.
simplify1(P, P) :-
is_atom(P), P \= (_ = _), P \= (_ \= _).
simplify1(P & Q, S) :-
flatten_op('&', [P,Q], TermsT),
simplify1_conjunction(TermsT, TermsS),
( TermsS = [] ->
S = true
;
% This will remove duplicates, which includes struct_equiv formulae
predsort(fml_compare, TermsS, Terms),
joinlist('&', Terms, S)
).
simplify1(P | Q, S) :-
flatten_op('|', [P, Q], TermsT),
simplify1_disjunction(TermsT, TermsS),
( TermsS = [] ->
S = false
;
% This will remove duplicates, which includes struct_equiv formulae
predsort(fml_compare, TermsS, Terms),
joinlist('|', Terms, S)
).
simplify1(P => Q, S) :-
simplify1(P, Sp),
simplify1(Q, Sq),
(
Sp=false -> S=true
;
Sp=true -> S=Sq
;
Sq=true -> S=true
;
Sq=false -> S=(~Sp)
;
S = (Sp => Sq)
).
simplify1(P <=> Q, S) :-
simplify1(P, Sp),
simplify1(Q, Sq),
(
struct_equiv(P, Q) -> S=true
;
struct_oppos(P, Q) -> S=false
;
Sp=false -> S=(~Sq)
;
Sq=true -> S=Sq
;
Sq=false -> S=(~Sp)
;
Sq=true -> S=Sp
;
S = (Sp <=> Sq)
).
simplify1(~P, S) :-
simplify1(P, SP),
(
SP=false -> S=true
;
SP=true -> S=false
;
SP = ~P2 -> S=P2
;
S = ~SP
).
simplify1(all(Xs, P), S) :-
( Xs = [] -> simplify1(P, S)
;
flatten_quant_and_simp(all, P, Xs, VarsT, Body),
sort(VarsT, Vars),
(
Body=false -> S=false
;
Body=true -> S=true
;
% Remove any useless variables
partition(ncontains_var(Body), Vars, _, Vars2),
( Vars2 = [] ->
S2 = Body
;
% Pull independent components outside the quantifier.
% Both conjuncts and disjuncts can be handled in this manner.
(flatten_op('|', [Body], BTerms), BTerms = [_,_|_] ->
partition(indep_of_vars(Vars), BTerms, Indep, BT2),
% Because we have removed useless vars, BT2 cannot be empty
joinlist('|', BT2, Body2),
( Indep = [] ->
S2=all(Vars2, Body2)
;
joinlist('|', Indep, IndepB),
S2=(all(Vars2, Body2) | IndepB)
)
; flatten_op('&', [Body], BTerms), BTerms = [_,_|_] ->
partition(indep_of_vars(Vars), BTerms, Indep, BT2),
joinlist('&', BT2, Body2),
( Indep = [] ->
S2=all(Vars2, Body2)
;
joinlist('&', Indep, IndepB),
S2=(all(Vars2, Body2) & IndepB)
)
;
S2=all(Vars2, Body)
)
),
S = S2
)).
simplify1(ext(Xs, P), S) :-
( Xs = [] -> simplify1(P, S)
;
flatten_quant_and_simp(ext, P, Xs, VarsT, Body),
sort(VarsT,Vars),
(
Body=false -> S=false
;
Body=true -> S=true
;
% Remove vars that are assigned a specific value, simply replacing
% them with their value in the Body formula
member(V1, Vars), var_valuated(V1, Body, Body2) ->
vdelete(Vars, V1, Vars2), simplify1(ext(Vars2, Body2), S)
;
% Remove any useless variables
partition(ncontains_var(Body), Vars, _, Vars2),
( Vars2 = [] ->
S = Body
;
% Pull independent components outside the quantifier,
% Both conjuncts and disjuncts can be handled in this manner.
(flatten_op('|', [Body], BTerms), BTerms = [_,_|_] ->
partition(indep_of_vars(Vars), BTerms, Indep, BT2),
joinlist('|', BT2, Body2),
( Indep = [] ->
S = ext(Vars2, Body2)
;
joinlist('|', Indep, IndepB),
S = (ext(Vars2, Body2) | IndepB)
)
; flatten_op('&', [Body], BTerms), BTerms = [_,_|_] ->
partition(indep_of_vars(Vars), BTerms, Indep, BT2),
joinlist('&', BT2, Body2),
( Indep = [] ->
S = ext(Vars2, Body2)
;
joinlist('&', Indep, IndepB),
S = (ext(Vars2, Body2) & IndepB)
)
;
S = ext(Vars2, Body)
)
)
)).
simplify1((A=B), S) :-
(
A == B -> S=true
;
% Utilising the unique names assumption, we can rewrite it to
% a conjunction of simpler equalities by striping functors, or
% to false if the terms will never unify
( unifiable(A, B, Eqs) ->
joinlist('&', Eqs, S1),
normalize(S1, S)
;
S=false
)
).
simplify1(knows(A, P), S) :-
simplify1(P, Ps),
( Ps=true -> S=true
; Ps=false -> S=false
; S = knows(A, Ps)
).
%
% simplify1_conjunction(In,Out) - simplify the conjunction of list of fmls
% simplify1_disjunction(In,Out) - simplify the disjunction of list of fmls
%
simplify1_conjunction(FmlsIn, FmlsOut) :-
maplist(simplify1, FmlsIn, FmlsI1),
simplify1_conjunction_rules(FmlsI1, FmlsI2),
simplify1_conjunction_acc(FmlsI2, [], FmlsOut).
simplify1_conjunction_rules(ConjsI, ConjsO) :-
% Pairwise try to apply rules for simplifying a conjunction.
(pairfrom(ConjsI, C1, C2, Rest),
(simplify1_conjunction_rule(C1,C2,C1o,C2o)
;
simplify1_conjunction_rule(C2,C1,C2o,C1o)) ->
simplify1_conjunction_rules([C1o,C2o|Rest],ConjsO)
;
ConjsO = ConjsI
).
simplify1_conjunction_rule(C1,C2,C1,C2o) :-
% (A & (B | ~A)) => (A & B)
% XXX TODO: flatten the disjunction?
C2 = (C2a | C2b),
( struct_oppos(C1,C2a), C2o=C2b
; struct_oppos(C1,C2b), C2o=C2a
).
simplify1_conjunction_rule(C1,C2,C1,true) :-
% (A & (B | A)) => A
% XXX TODO: flatten the disjunction?
C2 = (C2a | C2b),
( struct_equiv(C1,C2a)
; struct_equiv(C1,C2b)
).
simplify1_conjunction_acc([],FmlsAcc,FmlsAcc).
simplify1_conjunction_acc([F|FmlsIn],FmlsAcc,FmlsOut) :-
% Filter out obvious duplicates, or obvious negated-duplicates.
( member(Eq,FmlsAcc), struct_equiv(F,Eq) ->
F2 = true
; member(Opp,FmlsAcc), struct_oppos(F,Opp) ->
F2 = false
;
F2 = F
),
( F2=true ->
simplify1_conjunction_acc(FmlsIn,FmlsAcc,FmlsOut)
; F2=false ->
FmlsOut=[false]
;
simplify1_conjunction_acc(FmlsIn,[F2|FmlsAcc],FmlsOut)
).
simplify1_disjunction(FmlsIn,FmlsOut) :-
maplist(simplify1,FmlsIn,FmlsI1),
simplify1_disjunction_rules(FmlsI1,FmlsI2),
simplify1_disjunction_acc(FmlsI2,[],FmlsOut).
simplify1_disjunction_rules(DisjI,DisjO) :-
% Pairwise try to apply some simplification rules.
(pairfrom(DisjI,D1,D2,Rest),
(simplify1_disjunction_rule(D1,D2,D1o,D2o)
; simplify1_disjunction_rule(D2,D1,D2o,D1o)) ->
simplify1_disjunction_rules([D1o,D2o|Rest],DisjO)
;
DisjO = DisjI
).
simplify1_disjunction_rule(D1,D2,D1,D2o) :-
% A | (~A & B) => A | B
D2 = (D2a & D2b),
( struct_oppos(D1,D2a), D2o=D2b
; struct_oppos(D1,D2b), D2o=D2a
).
simplify1_disjunction_rule(D1,D2,D1,false) :-
% A | (A & B) => A
D2 = (D2a & D2b),
( struct_equiv(D1,D2a)
; struct_equiv(D1,D2b)
).
simplify1_disjunction_acc([],FmlsAcc,FmlsAcc).
simplify1_disjunction_acc([F|FmlsIn],FmlsAcc,FmlsOut) :-
% Filter out obvious duplicates, or obvious negated-duplicates.
( member(Eq,FmlsAcc), struct_equiv(F,Eq) ->
F2 = false
; member(Opp,FmlsAcc), struct_oppos(F,Opp) ->
F2 = true
;
F2 = F
),
( F2=false ->
simplify1_disjunction_acc(FmlsIn,FmlsAcc,FmlsOut)
; F2=true ->
FmlsOut=[true]
;
simplify1_disjunction_acc(FmlsIn,[F2|FmlsAcc],FmlsOut)
).
%
% var_given_value(X,P,V,Q) - variable X is uniformly given the value V
% within the formula P. Q is a formula equiv
% to P, with variable X set to V.
%
% var_given_value_list(X,Ps,V,Qs) - variable X is uniformly given the value
% V in all formulae in list Ps.
%
% Determining Q from P is not a simple substitution - if the value V
% contains vars that are introduced by a quantifier in P, this quantifier
% must be lifted to outermost scope.
%
var_given_value(X,A=B,V,true) :-
( X == A ->
V = B
;
X == B, V = A
).
var_given_value(X,P1 & P2,V,Q) :-
flatten_op('&',[P1,P2],Cjs),
select(Cj,Cjs,Rest), var_given_value(X,Cj,V,Qj),
partition(vgv_partition(X),Rest,Deps,Indeps),
(Indeps = [] -> IndepFml=true ; joinlist('&',Indeps,IndepFml)),
(Deps = [] -> DepFml1=true ; joinlist('&',Deps,DepFml1)),
subs(X,V,DepFml1,DepFml),
% We may have lifted a variable outside the scope of its
% quantifier. We must push QRest back down through the quantifiers
% to rectify this. By invariants of the operation, we know all
% relevant quantifiers are at outermost scope in Qj.
(DepFml \= true ->
term_variables(V,Vars),
vgv_push_into_quantifiers(Vars,Qj,DepFml,QFml)
;
QFml = Qj
),
Q = (IndepFml & QFml), !.
var_given_value(X,P1 | P2,V,Q) :-
flatten_op('|',[P1,P2],Djs),
var_given_value_list(X,Djs,V,Qs),
joinlist('|',Qs,Q).
var_given_value(X,all(Vars, P),V,all(VarsQ,Q)) :-
var_given_value(X,P,V,Q2),
flatten_quant(all,Q2,Vars,VarsQ,Q).
var_given_value(X,ext(Vars, P),V,ext(VarsQ,Q)) :-
var_given_value(X,P,V,Q2),
flatten_quant(ext,Q2,Vars,VarsQ,Q).
var_given_value(X,knows(A,P),V,knows(A,Q)) :-
var_given_value(X,P,V,Q).
% There's no clause for ~P because that can never give X a specific value
var_given_value_list(_,[],_,[]).
var_given_value_list(X,[H|T],V,[Qh|Qt]) :-
% Be careful not to do any unification on V.
% This ruins tail-recursion, but meh...
var_given_value(X,H,V,Qh),
var_given_value_list(X,T,V2,Qt),
V == V2.
vgv_partition(V,F) :-
contains_var(F,V).
% We can stop recursing either when Vars=[] or when we are
% no longer at a quantifier, since we assume all relevant
% quantifiers have been brought to the front.
vgv_push_into_quantifiers(Vars,ext(Qv, Qj),QDep,ext(Qv,Q)) :-
Vars \= [], !,
vgv_subtract(Vars,Qv,Vars2),
vgv_push_into_quantifiers(Vars2,Qj,QDep,Q).
vgv_push_into_quantifiers(Vars,all(Qv, Qj),QDep,all(Qv,Q)) :-
Vars \= [], !,
vgv_subtract(Vars,Qv,Vars2),
vgv_push_into_quantifiers(Vars2,Qj,QDep,Q).
vgv_push_into_quantifiers(_,Qj,QDep,Qj & QDep).
vgv_subtract([],_,[]).
vgv_subtract(Vs,[],Vs).
vgv_subtract(Vs,[X|Xs],Vs2) :-
vgv_subtract_helper(Vs,X,Vs1),
vgv_subtract(Vs1,Xs,Vs2).
vgv_subtract_helper([],_,[]).
vgv_subtract_helper([V|Vs],X,Vs2) :-
( X == V ->
vgv_subtract_helper(Vs,X,Vs2)
;
Vs2 = [V|Vs22],
vgv_subtract_helper(Vs,X,Vs22)
).
%
% var_valuated(X,P,P2) - variable X takes specific values throughout P,
% and P2 is P with the appropriate valuations
% inserted.
%
% In the base case, X is given a single value throughout the entire formula.
var_valuated(X,P,Q) :-
var_given_value(X,P,_,Q), !.
% The base case for P & Q - when they both give X the same value - is
% already covered by the var_valuated/3 clause above. But if one of the
% conjuncts is a disjunction that valuates X, then we can distribute over
% it to achieve a valuation.
var_valuated(X,P & Q,V) :-
flatten_op('&',[P,Q],Cjs),
select(Cj,Cjs,RestCjs),
flatten_op('|',[Cj],Djs),
maplist(var_valuated_check(X),Djs), !,
joinlist('&',RestCjs,RestFml),
var_valuated_distribute(X,Djs,RestFml,VDjs),
joinlist('|',VDjs,V), !.
var_valuated(X,P | Q,V) :-
flatten_op('|',[P,Q],Cs),
var_valuated_list(X,Cs,Vs),
joinlist('|',Vs,V).
var_valuated(X,all(V,P),all(V,Q)) :-
var_valuated(X,P,Q).
var_valuated(X,ext(V,P),ext(V,Q)) :-
var_valuated(X,P,Q).
var_valuated_list(_,[],[]).
var_valuated_list(X,[H|T],[Hv|Tv]) :-
var_valuated(X,H,Hv),
var_valuated_list(X,T,Tv).
var_valuated_distribute(_,[],_,[]).
var_valuated_distribute(X,[P|Ps],Q,[Pv|T]) :-
var_valuated(X,P & Q,Pv),
var_valuated_distribute(X,Ps,Q,T).
var_valuated_check(X,F) :-
%var_valuated(X,F,_).
var_given_value(X,F,_,_).
%
% copy_fml(P, Q) - make a copy of a formula. The copy will have all
% bound variables renamed to new vars. Any free variables
% will retain their original names.
%
copy_fml(P, P) :-
var(P), !.
copy_fml(P, P) :-
is_atom(P), !.
copy_fml(P & Q, R & S) :-
copy_fml(P, R),
copy_fml(Q, S).
copy_fml(P | Q, R | S) :-
copy_fml(P, R),
copy_fml(Q, S).
copy_fml(P => Q, R => S) :-
copy_fml(P, R),
copy_fml(Q ,S).
copy_fml(P <=> Q, R <=> S) :-
copy_fml(P, R),
copy_fml(Q, S).
copy_fml(~P, ~Q) :-
copy_fml(P, Q).
copy_fml(all(VarsP,P), all(VarsQ,Q)) :-
rename_vars(VarsP, P, VarsQ, P2),
copy_fml(P2, Q).
copy_fml(ext(VarsP,P), ext(VarsQ,Q)) :-
rename_vars(VarsP, P, VarsQ, P2),
copy_fml(P2, Q).
copy_fml(knows(A, P), knows(A, Q)) :-
copy_fml(P, Q).
%
% rename_vars(Vars,F,NewVars,NewF) - rename the given variables to new
% ones, producing a modified formula.
%
rename_vars(Vs, P, Vs2, P2) :-
rename_vars(Vs, P, [], Vs2, P2).
rename_vars([], P, Acc, Acc, P).
rename_vars([V|Vs], P, Acc, NewV, NewP) :-
subs(V, V2, P, P2),
append(Acc, [V2], Acc2),
rename_vars(Vs, P2, Acc2, NewV, NewP).
:- begin_tests(fluent,[sto(rational_trees)]).
test(simp1) :-
simplify(p & true, p).
test(simp2) :-
simplify(p & false, false).
test(simp3) :-
simplify(p | false, p).
test(simp4) :-
simplify(p | true, true).
test(simp5) :-
simplify(false | false, false).
test(simp6) :-
simplify(false | (p & ~(a=a)), false).
test(simp7) :-
simplify(true & true, true).
test(simp8) :-
simplify(all([X], p(X) & p(a)), all([X], p(X)) & p(a)).
test(simp9) :-
simplify(ext([X], p(X) & p(a)), ext([X], p(X)) & p(a)).
test(simp10) :-
X1 = ext([X], (
(p & (X=nil)) |
(q & (X=obs) & r ) |
(ext([Y], (s(Y) & (X=pair(a,Y)))))
)),
X2 = (p | (q & r) | ext([Y], s(Y))),
simplify(X1,X2).
test(val1) :-
var_given_value(X, X=a, a, true).
test(val2) :-
var_given_value(X, (X=a) & (X=b), b, F), simplify(F, false).
test(val3) :-
var_given_value(X, p(X) & q(a) & ext([Y], X=Y), Val, _),
Val == Y.
test(copy1) :-
F1 = all([X,Y], p(X) & r(Y)),
copy_fml(F1, F2),
F1 =@= F2,
F1 \== F2.
:- end_tests(fluent).
%
% sitcalc.pl: domain-independent sitcalc predicates.
%
% Copyright 2008-2014, Ryan Kelly
%
:- multifile(adp_fluent/3).
:- multifile(constraint/1).
%
% domain_prove/1 - reason relative to the domain axioms
% domain_prove_init/1 - reason relative to the domain axioms and initial
% conditions
%
domain_prove(Axs, Fml) :-
domain_preprocess_neg(Fml, PrepFml),
maplist(domain_preprocess, Axs, PrepAxs),
prove(PrepAxs, PrepFml).
domain_prove(Fml) :-
domain_axioms(Axs),
domain_prove(Axs, Fml).
domain_prove_init(Fml) :-
% For the initial situation, condition the query on the initial facts.
findall(I, initially(I), Inits),
joinlist('&', Inits, Init),
domain_axioms_init(Axs),
domain_prove(Axs, Init => Fml).
domain_axioms(Axs) :-
% The domain constraints must hold at every world,
% i.e. they are common knowledge.
findall(C, constraint(C), Axs).
domain_axioms_init(Axs) :-
% For the initial situation, treat all initially-known facts as axioms,
% i.e. they are common knowledge.
domain_axioms(Axs1),
findall(IK, initially_known(IK), Axs2),
append(Axs1, Axs2, Axs).
% Ensure that constraint/1 is defined even if the domain itself
% doesn't specify any constraints.
constraint(true).
%
% domain_preprocess/2 - pre-process formula for consumption by prover.
%
% The prover current doesn't accept existentially-quantified variables, so
% we have to pre-process and simplify the formula to remove them. It also
% doesn't support skolem functions, so our only option is to enumerate the
% possibilities and replace them with a disjunction.
%
% This predicate also does some other useful pre-processing steps to help
% the prover on its way:
%
% * Expands all([X,Y] P) into all(X, all(Y, P)) as expected by the prover
% * Replaces statically-known predicates with 'true' or 'false'
% * Simplifies the resulting formula
%
domain_preprocess(P, Q) :-
( is_literal(P) ->
% Don't pre-process literals, as this would replace statically-known
% predicates with 'true' or 'false' and remove them from axioms list.
Q = P
;
domain_preprocess(P, pos, R),
simplify(R, Q)
).
domain_preprocess_neg(P, Q) :-
( is_literal(P) ->
% Don't pre-process literals, as this would replace statically-known
% predicates with 'true' or 'false' and remove them from axioms list.
Q = P
;
domain_preprocess(P, neg, R),
simplify(R, Q)
).
reverse_polarity(pos, neg).
reverse_polarity(neg, pos).
reverse_polarity(any, any).
domain_preprocess(~P, Polarity, ~Q) :-
!,
reverse_polarity(Polarity, RevPolarity),
domain_preprocess(P, RevPolarity, Q).
domain_preprocess(P1 & Q1, Polarity, P2 & Q2) :-
!,
domain_preprocess(P1, Polarity, P2),
domain_preprocess(Q1, Polarity, Q2).
domain_preprocess(P1 | Q1, Polarity, P2 | Q2) :-
!,
domain_preprocess(P1, Polarity, P2),
domain_preprocess(Q1, Polarity, Q2).
domain_preprocess(P => Q, Polarity, R => S) :-
!,
reverse_polarity(Polarity, RevPolarity),
domain_preprocess(P, RevPolarity, R),
domain_preprocess(Q, Polarity, S).
domain_preprocess(P <=> Q, _, R <=> S) :-
!,
domain_preprocess(P, any, R),
domain_preprocess(Q, any, S).
domain_preprocess(knows(A, P), Polarity, knows(A, Q)) :-
!, domain_preprocess(P, Polarity, Q).
% Positively-occurring existential quantifers become a disjunction.
domain_preprocess(ext([], P), Polarity, Q) :-
!, domain_preprocess(P, Polarity, Q).
domain_preprocess(ext([X|Xs], P), neg, ext([X], Q)) :-
!, domain_preprocess(ext(Xs, P), neg, Q).
domain_preprocess(ext([X|Xs], P), Polarity, Q) :-
!,
( bagof(InstQ, domain_preprocess_enum(X, ext(Xs, P), Polarity, InstQ), Qs) ->
joinlist('|', Qs, Q)
;
Q = false
).
% Negatively-occurring universal quantifers become a conjunction.
domain_preprocess(all([], P), Polarity, Q) :-
!, domain_preprocess(P, Polarity, Q).
domain_preprocess(all([X|Xs], P), pos, all([X], Q)) :-
!, domain_preprocess(all(Xs, P), pos, Q).
domain_preprocess(all([X|Xs], P), Polarity, Q) :-
!,
( bagof(InstQ, domain_preprocess_enum(X, all(Xs, P), Polarity, InstQ), Qs) ->
joinlist('&', Qs, Q)
;
Q = true
).
% Primitive fluents that are statically known can be simplified away.
domain_preprocess(P, _, Q) :-
( ground(P) ->
( constraint(P) ->
Q = true
;
( constraint(~P) ->
Q = false
;
Q = P
)
)
;
Q = P
).
% Backtrack over all instanciations of Var in the given Fml.
domain_preprocess_enum(Var, Fml, Polarity, Inst) :-
( infer_var_type(Var, Fml, Type) ->
true
;
write(failed_to_infer_var_type(Var, Fml)), nl, fail
),
% this backtracks over the different values
call(Type, Value),
subs(Var, Value, Fml, Inst0),
% this may replace statically-known facts with 'true' or 'false'
domain_preprocess(Inst0, Polarity, Inst1),
% and this may simplify the resulting formulae based on the replacements
simplify(Inst1, Inst).
% Infer the type of a variable, based on its use in the formula.
infer_var_type(V, ~P, T) :-
!, infer_var_type(V, P, T).
infer_var_type(V, P & Q, T) :-
!, ( infer_var_type(V, P, T) -> true ; infer_var_type(V, Q, T) ).
infer_var_type(V, P | Q, T) :-
!, ( infer_var_type(V, P, T) -> true ; infer_var_type(V, Q, T) ).
infer_var_type(V, P => Q, T) :-
!, ( infer_var_type(V, P, T) -> true ; infer_var_type(V, Q, T) ).
infer_var_type(V, P <=> Q, T) :-
!, ( infer_var_type(V, P, T) -> true ; infer_var_type(V, Q, T) ).
infer_var_type(V, all(_, P), T) :-
!, infer_var_type(V, P, T).
infer_var_type(V, ext(_, P), T) :-
!, infer_var_type(V, P, T).
infer_var_type(V, knows(_, P), T) :-
!, infer_var_type(V, P, T).
infer_var_type(V, P, T) :-
P =.. [F|Args],
findmember(V, Args, Idx),
length(Args, N),
length(Types, N),
Tmplt =.. [F|Types],
prim_fluent(Tmplt),
nth0(Idx, Types, T).
% XXX TODO: infer by equality with another term of inferrable type?
%
% adp_fluent(F, A, C) - C is the defn for ADP fluent F applied to action A
%
% The specific ADP fluent definitions are given in domain.pl, but we give
% a default implementation for the case when A is a variable, which simply
% enumerates each possible action and conjoins the individual definitions.
%
adp_fluent(F, Act, Defn) :-
var(Act), !,
(bagof(Ft, adp_fluent_enum_actions(F, Act, Ft), Fts) ->
joinlist(('|'), Fts, Ftmp),
simplify(Ftmp, Defn)
;
Defn = F
).
adp_fluent_enum_actions(F, Act, Defn) :-
term_with_vars(prim_action, Act1, V),
adp_fluent(F, Act1, Defn1),
Defn = ext(V, (Defn1 & (Act=Act1))).
%
% Useful ADPs that can be defined in terms of other, simpler ADPs
%
adp_fluent(pbu(Agt), Act, Defn) :-
adp_fluent(poss, Act, Poss),
adp_fluent(unobs(Agt), Act, Unobs),
simplify(Poss & Unobs, Defn).
adp_fluent(obs(Agt, Obs), Act, Defn) :-
% We don't reify sets of observations as terms since that would greatly
% complicate the prover. Rather we treat "obs(Agt, O, S)" as an ADP
% stating whether a specific observation O is observed by agent Agt in
% situation S. The domain definition should enumerate all the concrete
% cases, and this rule closes over them to handle the general case
% where O is unbound.
var(Obs), !,
(bagof(DefnN, adp_fluent_enum_obs(obs(Agt, Obs), Act, DefnN), Defns) ->
joinlist(('|'), Defns, Defn1),
simplify(Defn1, Defn)
;
Defn = false
).
adp_fluent_enum_obs(obs(Agt, Obs), Act, Defn) :-
term_with_vars(prim_observation, Obs1, Vars),
adp_fluent(obs(Agt, Obs1), Act, Defn1),
Defn = ext(Vars, (Obs=Obs1) & Defn1).
adp_fluent(unobs(Agt), Act, Defn) :-
(bagof(DefnN, adp_fluent_enum_unobs(unobs(Agt), Act, DefnN), Defns) ->
joinlist(('|'), Defns, Defn1),
simplify(~Defn1, Defn)
;
Defn = true
).
adp_fluent_enum_unobs(unobs(Agt), Act, Defn) :-
term_with_ground_args(prim_observation, Obs),
adp_fluent(obs(Agt, Obs), Act, Defn).
%
% regression(+F, +A, -Fr) - Fr is the regression of F over action A.
%
% This predicate calculates the regression of a fluent F with respect to
% an action A, yielding a new fluent Fr. If A is free, it will consider all
% types of action that could affect the fluent.
%
% If A is non-free, regression1 will succeed exactly once.
regression(F, A, Fr) :-
nonvar(A), !,
regression1(F, A, Frt),
simplify(Frt, Fr).
% If A is free, find all actions which could affect F.
regression(F, A, Fr) :-
var(A), !,
(bagof(Ft, A1^regression_enum_actions(F, A, A1, Ft), Fts) ->
joinlist(('|'), Fts, Fr1),
simplify(Fr1, Fr)
;
Fr = F
).
regression_enum_actions(F, AVar, ATerm, Fr) :-
term_with_vars(prim_action, ATerm, V),
regression(F, ATerm, Fr1),
Fr = ext(V, (Fr1 & (AVar=ATerm))).
% Regression base case, a primitive fluent.
% Build successor state axiom from causes_true/cases_false
regression1(F, A, Fr) :-
is_atom(F), F \= (_ = _),
(causes_true(F, A, Ep) -> true ; Ep = false),
(causes_false(F, A, En) -> true ; En = false),
simplify(Ep | (F & ~En), Fr).
% No functional fluents, so equality is rigid
regression1(T1=T2, _, T1=T2).
% Regression is pushed inside the logical operators
regression1(all(X, P), A, all(X, R)) :-
regression1(P, A, R).
regression1(ext(X, P), A, ext(X, R)) :-
regression1(P, A, R).
regression1(~P, A, ~R) :-
regression1(P, A, R).
regression1((P & Q), A, (R & S)) :-
regression1(P, A, R),
regression1(Q, A, S).
regression1((P | Q), A, (R | S)) :-
regression1(P, A, R),
regression1(Q, A, S).
regression1((P => Q), A, (R => S)) :-
regression1(P, A, R),
regression1(Q, A, S).
regression1((P <=> Q), A, (R <=> S)) :-
regression1(P, A, R),
regression1(Q, A, S).
% Regression of a knowledge expression.
% For the simple finite domains we deal with here, it's better to
% explicitly enumerate the potential observations and split by cases
% rather than try to produce a generic knowledge expression.
regression1(knows(Agt, P), Act, Fr) :-
% Calculate the required persistence condition.
pcond(P, pbu(Agt), PCond),
% Enumerate all the different sets of observations that might occur
% as a result of this action, including the empty set. This really
% only works when there is a small number of potential observations...
findall(OSet, regression1_knows_enum_obs_sets(Agt, Act, OSet), OSetL),
% For each such set, regress assuming that's what was observed.
maplist(regression1_knows_obs_set(Agt, P, PCond, Act), OSetL, RKnowsL),
% The overall knowledge is the disjunction all all cases,
% since we're expanding existential quantification over obs sets.
joinlist('|', RKnowsL, RKnows),
simplify(RKnows, Fr).
regression1_knows_enum_obs_sets(Agt, Act, Obs:NObs) :-
findall(O, regression1_knows_enum_obs(Agt, Act, O), AllOs),
regression1_knows_split_subsets(AllOs, Obs, NObs).
regression1_knows_enum_obs(Agt, Act, O) :-
term_with_ground_args(prim_observation, O),
adp_fluent(obs(Agt, O), Act, Defn),
simplify(Defn, DefnS),
DefnS \= false.
regression1_knows_split_subsets([], [], []).
regression1_knows_split_subsets([H|T], Incl, Excl) :-
(
Excl = [H|Rest],
regression1_knows_split_subsets(T, Incl, Rest)
;
Incl = [H|Rest],
regression1_knows_split_subsets(T, Rest, Excl)
).
regression1_knows_obs_set(Agt, P, PC, Act, OSet, RKnows) :-
% Regress knows(Agt, P) assuming that the observations set is exactly
% as specified by Obs:NObs, i.e. the things in Obs are observed and the
% things in NObs are not observed.
Obs:NObs = OSet,
% First, figure out what holds in the world to cause this observations.
regression1_knows_obs_set_defn(Agt, Act, Obs:NObs, ObsCond),
% Split on whether the set of observations was empty.
( Obs = [] ->
% If so, then the state of knowledge must be unchanged.
RKnows = ObsCond & knows(Agt, P)
;
% If not, we need to split on each possible action that could
% match those observations.
(bagof(RK, regression1_knows_obs_set_enum_act(Agt, PC, OSet, RK), RKs) ->
% The overall knowledge is the conjunction of these cases,
% since we're expanding universal quantification over actions.
joinlist('&', RKs, RK),
simplify(ObsCond & RK, RKnows)
;
% If there are no action that could match those observations,
% something has gone terribly wrong with the agent's knowledge...
RKnows = ObsCond & knows(Agt, false)
)
).
regression1_knows_obs_set_defn(Agt, Act, Obs:NObs, Defn) :-
maplist(regression1_knows_obs_defn(Agt, Act), Obs, ObsDefnL),
maplist(regression1_knows_nobs_defn(Agt, Act), NObs, NObsDefnL),
( Obs = [] -> ObsDefn = true ; joinlist('&', ObsDefnL, ObsDefn) ),
( NObs = [] -> NObsDefn = true ; joinlist('&', NObsDefnL, NObsDefn) ),
simplify(ObsDefn & NObsDefn, Defn).
regression1_knows_obs_defn(Agt, Act, O, Defn) :-
( adp_fluent(obs(Agt, O), Act, Defn) -> true ; Defn=false ).
regression1_knows_nobs_defn(Agt, Act, O, ~Defn) :-
regression1_knows_obs_defn(Agt, Act, O, Defn).
regression1_knows_obs_set_enum_act(Agt, PCond, Obs:NObs, RKnows) :-
% For every potential action Act', we must know that either:
% it is not possible, or
% it produces different observations to the set given, or
% R(PCond, Act') holds
term_with_ground_args(prim_action, Act),
adp_fluent(poss, Act, PossCond),
regression1_knows_obs_set_defn(Agt, Act, Obs:NObs, ObsCond),
regression(PCond, Act, RPCond),
simplify(~PossCond | ~ObsCond | RPCond, RKnows).
% Knowledge fluents need an extra regression step once we reach the
% initial situation.
%
regression_s0(F, F) :-
is_atom(F).
regression_s0(all(X, P), all(X, R)) :-
regression_s0(P, R).
regression_s0(ext(X, P), ext(X, R)) :-
regression_s0(P, R).
regression_s0(~P, ~R) :- !,
regression_s0(P, R).
regression_s0((P & Q), (R & S)) :-
regression_s0(P, R),
regression_s0(Q ,S).
regression_s0((P | Q), (R | S)) :-
regression_s0(P, R),
regression_s0(Q, S).
regression_s0((P => Q), (R => S)) :-
regression_s0(P, R),
regression_s0(Q, S).
regression_s0((P <=> Q), (R <=> S)) :-
regression_s0(P, R),
regression_s0(Q, S).
regression_s0(knows(Agt, P), knows(Agt, PCond)) :-
pcond(P, pbu(Agt), PCond).
%
% holds(+F, +S) - fluent F holds in situation S
%
% This predicate is true whenever the fluent F holds in situation S. It
% is evaluated by regressing over the action terms in S until it reaches
% the initial situation. The regressed formula is then evaluated against
% the defined properties of the initial situation.
%
holds(F, do(A, S)) :-
!,
regression(F, A, Fr),
holds(Fr, S).
holds(F, s0) :-
regression_s0(F, Fr),
domain_prove_init(Fr).
%
% pcond(F, ADP, P) - persistence condition for F under ADP.
%
% The basic meaning of this pedicate is: if fluent P holds in situation
% s, then fluent F will hold in s and in all successors of s reachable by
% performing actions that satisfy ADP.
%
% It is implemented as a simple fixpoint of pcond_d1/3.
%
pcond(F, ADP, P) :-
(domain_prove(~F) ->
P = false
; domain_prove(F) ->
P = true
;
pcond_acc_fixpoint(F, ADP, true, P1),
simplify(P1, P)
).
pcond_acc_fixpoint(P1Prev, ADP, PAccum, P) :-
pcond_d1(P1Prev, ADP, P1Next),
(domain_prove(~P1Next) ->
P = false
; domain_prove(P1Next) ->
P = P1Prev & PAccum
;
PAccum2 = P1Prev & PAccum,
(domain_prove(PAccum2 => P1Next) ->
P = PAccum2
;
pcond_acc_fixpoint(P1Next, ADP, PAccum2, P)
)
).
%
% pcond_d1(F, ADP, P1) - depth 1 persistence condition for fluent F
%
% The basic meaning of this pedicate is: if fluent F holds in situation
% s, then it will continue to hold in all ADP-successors of s as long
% as P1 is true in s.
%
pcond_d1(F, ADP, P1) :-
( bagof(Defn, pcond_d1_enum_actions(F, ADP, Defn), Defns) ->
joinlist('&', Defns, P1t),
simplify(P1t, P1)
;
P1=true
).
pcond_d1_enum_actions(F, ADP, PDefn) :-
term_with_ground_args(prim_action, A),
regression(F, A, Fr),
( struct_equiv(F, Fr) ->
PDefn = true
;
adp_fluent(ADP, A, Defn),
( domain_prove(F => ~Defn) ->
PDefn = true
;
PDefn = (Fr | ~Defn)
)
).
%
% term_with_vars(Type, Term, Vars) - instantiate a term with variable args.
%
% Given a type predicate Type, this predicate binds Term to one of the
% solutions of that predicate and Vars to a list of the free variables
% in the term. It is used for enumerating each of the finite set of e.g.
% action types in the domain:
%
% term_with_vars(prim_action, A, Vars)
%
term_with_vars(Type, Term, Vars) :-
call(Type, TypedTerm),
TypedTerm =.. [Functor|ArgTypes],
term_with_vars_collect(ArgTypes, Vars),
Term =.. [Functor|Vars].
term_with_vars_collect([], []).
term_with_vars_collect([_|Ts], [_|Vs]) :-
term_with_vars_collect(Ts, Vs).
term_with_ground_args(Type, Term) :-
call(Type, TypedTerm),
TypedTerm =.. [Functor|ArgTypes],
maplist(call, ArgTypes, Args),
Term =.. [Functor|Args].
% :- [(domain_wumpus)].
%
% Domain-specific definitions.
%
% Copyright 2008-2014, Ryan Kelly
%
% This axiomatisation is for the "multi-agent hunt the wumpus"" domain from
% the paper "Asynchronous Knowledge with Hidden Actions in the Situation
% Calculus" by Ryan F Kelly and Adrian R Pearce.
%
:- discontiguous(causes_true/3).
:- discontiguous(causes_false/3).
:- multifile(adp_fluent/3).
% Enumerate the values of the various object types in the domain
agent(ann).
agent(bob).
room(room1).
room(room2).
room(room3).
room(room4).
room(room5).
room(room6).
room(room7).
room(room8).
room(room9).
adjacent(room1, room2).
adjacent(room1, room4).
adjacent(room2, room1).
adjacent(room2, room3).
adjacent(room2, room5).
adjacent(room3, room2).
adjacent(room3, room6).
adjacent(room4, room1).
adjacent(room4, room5).
adjacent(room4, room7).
adjacent(room5, room2).
adjacent(room5, room4).
adjacent(room5, room6).
adjacent(room5, room8).
adjacent(room6, room3).
adjacent(room6, room5).
adjacent(room6, room9).
adjacent(room7, room4).
adjacent(room7, room8).
adjacent(room8, room5).
adjacent(room8, room7).
adjacent(room8, room9).
adjacent(room9, room6).
adjacent(room9, room8).
% Enumerates primitive actions, and the types of their arguments.
prim_action(move(agent, room)).
prim_action(shoot(agent, room)).
prim_action(alert(agent)).
% Enumerates primitive observation terms, and the types of their arguments.
prim_observation(move(agent, room)).
prim_observation(steps).
prim_observation(shoot(agent, room)).
prim_observation(alert).
prim_observation(stench).
prim_observation(scream).
% Enumerates primitive fluents, and types of arguments
prim_fluent(in(agent, room)).
prim_fluent(wumpus(room)).
prim_fluent(stench(room)).
prim_fluent(adjacent(room, room)).
prim_fluent(killed).
% Definitions for action description predicate fluents
% Possibility.
adp_fluent(poss, move(Agt, Room),
ext([R], in(Agt, R) & adjacent(R, Room))
).
adp_fluent(poss, shoot(Agt, Room),
ext([R], in(Agt, R) & adjacent(R, Room))
).
adp_fluent(poss, alert(Agt),
ext([R], in(Agt, R) & stench(R))
).
% Observations.
adp_fluent(obs(Agt, move(Agt1, Room1)), move(Agt2, Room2),
% Full move action is observable if...
(Room1=Room2) & (Agt1=Agt2) & (
% the observer is in the destination room
in(Agt, Room1)
|
% or the observer is in the source room.
ext([Room3], in(Agt, Room3) & in(Agt1, Room3))
)
).
adp_fluent(obs(Agt, steps), move(Agt1, Room1),
% Footsteps can be heard when someone moves if...
ext([Room2], (in(Agt, Room2) & (
% the observer is adjacent to the destination room
adjacent(Room2, Room1)
|
% or the observer is adjacent to the source room.
ext([Room3], in(Agt1, Room3) & adjacent(Room2, Room3))
)))
).
adp_fluent(obs(Agt, shoot(Agt1, Room1)), shoot(Agt2, Room2),
% Full shoot action is observable if...
(Room1=Room2) & (Agt1=Agt2) & (
% the observer is in the target room
in(Agt, Room1)
|
% or the observer is in the source room.
ext([Room3], in(Agt, Room3) & in(Agt1, Room3))
)
).
adp_fluent(obs(Agt, alert), alert(Agt1),
% An alert can be heard if...
ext([Room, Room1], (
in(Agt, Room) & in(Agt1, Room1) & (
% the observer is in the same room as the announcer
(Room = Room1)
|
% or the observer is in a room adjacent to the announcer
adjacent(Room, Room1)
)
))
).
adp_fluent(obs(Agt, stench), move(Agt1, Room1),
% A stench is observed by anyone entering a stench-filled room.
(Agt=Agt1) & stench(Room1)
).
adp_fluent(obs(_, scream), shoot(_, Room1),
% Everyone hears the scream if the wumpus is shot.
wumpus(Room1)
).
% Causal rules for each fluent/action combo
causes_true(in(Agt, Room), move(Agt2, Room2),
(Agt=Agt2) & (Room=Room2)
).
causes_false(in(Agt, Room), move(Agt2, Room2),
(Agt=Agt2) & ~(Room=Room2)
).
causes_true(killed, shoot(_, Room),
wumpus(Room)
).
% Specify what holds in the initial situation.
% The wumpus is in room five, but this is not known to the agents.
initially(wumpus(room5)).
% The agents are known to start in the entry room.
initially_known(in(Agt, room1)) :-
agent(Agt).
% The wumpus is known to start out alive.
initially_known(~killed).
% Specify the constraints.
% These are true in all situations and hence are common knowledge.
% They form the background theory of the domain.
% There's nothing suspicious about the entry room.
constraint(~wumpus(room1)).
constraint(~stench(room1)).
% The cave layout is fixed, according to adjacency definitions.
constraint(adjacent(R1, R2)) :-
room(R1), room(R2), adjacent(R1, R2).
constraint(~adjacent(R1, R2)) :-
room(R1), room(R2), \+ adjacent(R1, R2).
% Exactly one room contains the wumpus.
constraint(all([R1,R2], (wumpus(R1) & wumpus(R2)) => (R1=R2))).
constraint(ext([R], wumpus(R))).
% Each agent is in exactly one room.
% XXX TODO: including these tips the scales into too much exponential
% branching during proof search.
%constraint(all([R1,R2], (in(Agt, R1) & in(Agt, R2)) => (R1=R2))) :-
% agent(Agt).
%constraint(ext([R], in(Agt, R))) :-
% agent(Agt).
% A room has a stench iff the wumpus is in that room or in an adjacent one.
constraint(all([R1], (
stench(R1) => (wumpus(R1) | ext([R2], (wumpus(R2) & adjacent(R1, R2))))
))).
constraint(all([R1], (
(wumpus(R1) | ext([R2], (wumpus(R2) & adjacent(R1, R2)))) => stench(R1)
))).
%
% And now for the unit tests...
%
:- begin_tests(domain_wumpus,[sto(rational_trees)]).
test(sanity1) :-
domain_prove(~wumpus(room1)),
domain_prove(all([R], adjacent(room1, R) => ~wumpus(R))),
%domain_prove(in(bob, room1) => ~in(bob, room2)),
true.
test(example0) :-
holds(in(ann, room1), s0),
holds(in(bob, room1), s0),
%holds(knows(ann, in(bob, room1)), s0),
%holds(~ext([X], knows(ann, wumpus(X))), s0),
%holds(knows(ann, ~wumpus(room1)), s0),
%holds(knows(ann, ~wumpus(room2)), s0),
%holds(knows(ann, ~wumpus(room4)), s0),
true. %\+ holds(knows(ann, ~wumpus(room5)), s0).
:- end_tests(domain_wumpus).
%:- [(domain_party)].
%
% Domain-specific definitions.
%
% Copyright 2008-2014, Ryan Kelly
%
% This axiomatisation is for the "party invitation"" domain from the
% PhD thesis "Asynchronous Multi-Agent Reasoning in the Situation Calculus"
% by Ryan F Kelly.
%
:- discontiguous(causes_true/3).
:- discontiguous(causes_false/3).
:- multifile(adp_fluent/3).
% Enumerate the values of the various object types in the domain
agent(ann).
agent(bob).
location(cathys_house).
location(dannys_house).
% Enumerates primitive actions, and the types of their arguments.
prim_action(read(agent)).
prim_action(leave(agent)).
prim_action(enter(agent)).
% Enumerates primitive observation terms, and the types of their arguments.
prim_observation(read(agent)).
prim_observation(leave(agent)).
prim_observation(enter(agent)).
prim_observation(party_at(location)).
% Enumerates primitive fluents, and types of arguments
prim_fluent(inroom(agent)).
prim_fluent(party_at(location)).
% Definitions for action description predicate fluents
% Possibility.
adp_fluent(poss, read(Agt), inroom(Agt)).
adp_fluent(poss, enter(Agt), ~inroom(Agt)).
adp_fluent(poss, leave(Agt), inroom(Agt)).
% Observations.
adp_fluent(obs(Agt, read(Agt1)), read(Agt2), (Agt1=Agt2) & (Agt1=Agt | inroom(Agt))).
adp_fluent(obs(_, enter(Agt1)), enter(Agt2), Agt1=Agt2).
adp_fluent(obs(_, leave(Agt1)), leave(Agt2), Agt1=Agt2).
adp_fluent(obs(Agt, party_at(Loc)), read(Agt1), (Agt=Agt1) & party_at(Loc)).
% Causal rules for each fluent/action combos
causes_true(inroom(Agt1), enter(Agt2), Agt1=Agt2).
causes_false(inroom(Agt1), leave(Agt2), Agt1=Agt2).
% Specify what holds in the initial situation.
initially(party_at(cathys_house)).
initially(~party_at(dannys_house)).
initially(~knows(Agt, party_at(Loc))) :-
agent(Agt), location(Loc).
initially(knows(Agt1, ~knows(Agt2, party_at(Loc)))) :-
agent(Agt1), agent(Agt2), location(Loc).
initially_known(inroom(ann)).
initially_known(inroom(bob)).
initially_known(party_at(cathys_house) | party_at(davids_house)).
%
% And now for the unit tests...
%
:- begin_tests(domain_party, [sto(rational_trees)]).
test(reg1) :-
regression(inroom(ann), read(bob), inroom(ann)).
test(reg2) :-
regression(inroom(ann), enter(bob), inroom(ann)).
test(reg3) :-
regression(inroom(ann), leave(bob), inroom(ann)).
test(reg4) :-
regression(inroom(ann), enter(ann), true).
test(reg5) :-
regression(inroom(ann), leave(ann), false).
test(adp1) :-
adp_fluent(obs(ann, read(ann)), O, O=read(ann)).
test(adp2) :-
adp_fluent(obs(ann, read(bob)), O, inroom(ann) & (O=read(bob))).
%@TODO
test(adp3) :-
adp_fluent(pbu(ann), read(bob), inroom(bob)& ~inroom(ann)).
test(holds1) :-
holds(inroom(ann), s0).
%@TODO
test(holds2, fail) :-
holds(~inroom(ann), s0).
test(holds3) :-
holds(~inroom(ann), do(leave(ann), s0)), !.
test(holds4) :-
holds(inroom(ann), do(leave(bob), s0)), !.
test(holds5) :-
holds(ext([X], inroom(X)), do(leave(bob), s0)), !.
test(holds6) :-
holds(all([X], inroom(X)), s0).
%@TODO
test(holds7) :-
\+ holds(all([X], inroom(X)), do(leave(bob), s0)).
test(holds8) :-
holds(party_at(cathys_house), s0).
test(knows1) :-
holds(knows(ann, inroom(ann)), s0), !.
test(knows2_p) :-
holds(knows(ann, inroom(bob)), s0), !.
test(knows3) :-
holds(knows(bob, ~inroom(ann)), do(leave(ann), s0)), !.
test(knows4) :-
holds(~knows(bob, inroom(ann)), do(leave(ann), s0)), !.
%@TODO
test(knows6_p) :-
\+ holds(knows(bob, party_at(cathys_house)), s0).
test(example1) :-
% Initially, ann does not know where the party is.
holds(~ ext([L], knows(ann, party_at(L))), s0), !.
test(example2) :-
% Bob knows the true location of the party after reading the invite.
holds(knows(bob, party_at(cathys_house)), do(read(bob), s0)), !.
test(example3) :-
% Bob knows that ann does not know where the party is.
holds(knows(bob, ~knows(ann, party_at(cathys_house))), s0).
test(example4) :-
% After leaving the room, bob no longer knows that
% ann does not know where the party is.
holds(~knows(bob, ~knows(ann, party_at(cathys_house))),
do(leave(bob), s0)), !.
:- end_tests(domain_party).
% :- run_tests.
| TeamSPoon/logicmoo_workspace | packs_sys/logicmoo_agi/prolog/abduction/adv_mindi2.pl | Perl | mit | 80,305 |
#!/usr/bin/env perl
use warnings;
use strict;
use Getopt::Long;
use YAML::XS qw(LoadFile DumpFile);
use Assembly::Utils;
# Keep all files for best kmer (trim and raw)
# Remove all but contigs.fa, Log, and Roadmaps files for others.
# Do not touch folders with files less than one day old - may still be processing
# Future: compression of Roadmaps/contigs for non-best.
# Future: removal of all but Log file for poor (e.g. <2000) N50's
# Future: support for inclusion of other 'bests' e.g. max contig length.
# Note: we assume all of the stats are in the input yaml file and
# do not explicitly parse the VelvetStats.tab file.
my $options = {};
my @del_files = qw(CnyUnifiedSeq.names Roadmaps stats.txt LastGraph);
# push (@del_files, "CnyUnifiesSeq");
# push (@del_files, "Graph2")
# push (@del_files, "PreGraph");
sub set_default_opts
{
my %defaults = qw(
yaml_in yaml_files/12_velvet_stats.yml
verbose 1
run 0
);
for my $kdef (keys %defaults) {
$options->{$kdef} = $defaults{$kdef} unless $options->{$kdef};
}
}
sub check_opts
{
unless ($options->{yaml_in}) {
die "Usage: $0 -i <input yaml file>
Optional:
--verbose
--run
";
}
}
sub gather_opts
{
$options->{qsub_opts} = '';
GetOptions($options,
'yaml_in|i=s',
'yaml_out|o=s',
'verbose',
'run',
);
set_default_opts;
check_opts;
}
sub print_verbose
{
if ($options->{verbose}) {
print (@_);
}
}
sub remove_files
{
my $rec = shift;
my $kmer = shift;
my $kdir = Assembly::Utils::get_check_record($rec, ["kmer", $kmer, "kmer_dir"]);
if ($kdir and -e $kdir) {
for my $fname (@del_files) {
my $fpath = $kdir . "/" . $fname;
if (-e $fpath and (-M $fpath >= 1)) {
print_verbose("Removing file $fpath\n");
if ($options->{run}) {
system ("rm $fpath");
}
} else {
print_verbose("No such file or file modified within the past 24 hours: $fpath\n");
}
}
}
}
sub remove_range
{
my $rec = shift;
my $kmin = Assembly::Utils::get_check_record($rec, ["min_kmer"]);
my $kmax = Assembly::Utils::get_check_record($rec, ["max_kmer"]);
my $best_kmer = Assembly::Utils::get_check_record($rec, ["max_n50_kmer"]);
if ($best_kmer and $kmin and $kmax) {
for (my $k = $kmin; $k <= $kmax; $k += 2) {
if ($k != $best_kmer) {
remove_files($rec, $k);
}
}
} else {
print_verbose "Could not determine best/min/max kmers for this record";
}
}
sub remove_all
{
my $records = shift;
for my $species (keys %$records) {
for my $strain (keys %{$records->{$species}->{DNA}}) {
for my $trimraw (qw(trim raw)) {
print "species $species strain $strain trimraw $trimraw\n";
my $rec = Assembly::Utils::get_check_record($records, [$species, "DNA", $strain, "velvet", $trimraw]);
if ($rec) {
remove_range($rec);
} else {
print_verbose "Could not get YAML record for species $species strain $strain trim/raw: $trimraw\n";
}
}
}
}
}
gather_opts;
my $records = LoadFile($options->{yaml_in});
remove_all($records);
| AAFC-MBB/crti-assembly-pipeline | VelvetCleanup.pl | Perl | mit | 3,476 |
/*******************************************************************************
Filename: adventure.pl
Author: David C. Drake (https://davidcdrake.com)
Description: "I USED TO BE AN ADVENTURER LIKE YOU": A simple text adventure
game utilizing the Prolog programming language. Your goal is to
find the treasure without dying or taking an arrow in the knee.
*******************************************************************************/
/* location descriptions */
description(valley,
'You are in a valley with a trail stretching out before you.').
description(path,
'You are on a narrow path with ravines on either side.').
description(cliff,
'You are teetering on the edge of a cliff.').
description(fork,
'You are at a fork in the path.').
description(maze(_),
'You are in a maze of twisty little passages, all alike.').
description(mountaintop,
'You are on a snowy mountaintop.').
/* report = print the current location's description */
report :-
at(you,X),
description(X,Y),
write(Y),
nl.
/* connect(X,Dir,Y) = if at X and moving in direction Dir, go to Y */
connect(valley,forward,path).
connect(path,right,cliff).
connect(path,left,cliff).
connect(path,forward,fork).
connect(fork,left,maze(0)).
connect(fork,right,mountaintop).
connect(maze(0),left,maze(1)).
connect(maze(0),right,maze(3)).
connect(maze(1),left,maze(0)).
connect(maze(1),right,maze(2)).
connect(maze(2),left,fork).
connect(maze(2),right,maze(0)).
connect(maze(3),left,maze(0)).
connect(maze(3),right,maze(3)).
/* move(Dir) = move the player in direction Dir, then print a description */
move(Dir) :-
at(you,Loc),
connect(Loc,Dir,Next),
retract(at(you,Loc)),
assert(at(you,Next)),
report,
!.
move(_) :-
write('That is not a legal move.\n'),
report.
/* treasure = if found, the player wins */
treasure :-
at(treasure,Loc),
at(you,Loc),
write('You have found the treasure. Congratulations, you win!\n'),
retract(at(you,Loc)),
assert(at(you,done)),
!.
treasure. % Otherwise, nothing happens.
/* archer = if the player and archer are at the same location, game over */
archer :-
at(archer,Loc),
at(you,Loc),
write('You take an arrow in the knee. Your adventuring days are over.\n'),
retract(at(you,Loc)),
assert(at(you,done)),
!.
archer. % Otherwise, nothing happens.
/* cliff = if the player is at the cliff, game over */
cliff :-
at(you,cliff),
write('You fall off the edge. Your adventuring days are over.\n'),
retract(at(you,cliff)),
assert(at(you,done)),
!.
cliff. % Otherwise, nothing happens.
/* main = while not done, get moves from the player, check state, repeat */
main :-
at(you,done),
!.
main :-
write('\nNext move: '),
read(Move),
nl,
call(Move),
treasure,
archer,
cliff,
main.
/* start = starting point for the game */
start :-
retractall(at(_,_)), % clean up from previous runs
assert(at(you,valley)),
assert(at(archer,maze(3))),
assert(at(treasure,mountaintop)),
write('\nWelcome to the I USED TO BE AN ADVENTURER LIKE YOU game!\n'),
write('Legal commands: "left.", "right.", and "forward."\n'),
write('(Each command must end with a period.)\n\n'),
report,
main.
/* additional commands */
forward :- move(forward).
left :- move(left).
right :- move(right).
begin :- start.
play :- start.
go :- start.
| theDrake/prolog-experiments | adventure.pl | Perl | mit | 3,358 |
#!/usr/bin/env perl
use v5.18;
use strict;
use warnings;
use List::Util qw(max);
use Getopt::Long qw(GetOptions);
use Mojo::JSON qw(decode_json);
use Mojo::IOLoop;
use Mojo::Util;
use Mojo::IRC;
use Mojo::IRC::UA;
use IRC::Utils ();
use WWW::Telegram::BotAPI;
my $CONTEXT = {};
sub message_from_tg_to_irc {
state $last_sent_text = "";
my $channel = $CONTEXT->{irc_channel} or return;
my $irc = $CONTEXT->{irc_bot} or return;
my ($tg_message) = @_;
if ($tg_message->{text} && $tg_message->{text} ne "") {
my @lines = grep { ! /^\s+$/ } split /\n+/, $tg_message->{text};
for my $line (@lines) {
my $from_name = $tg_message->{from}{username} // $tg_message->{from}{first_name};
my $text = '<' . $from_name . '> ';
if ($tg_message->{reply_to_message}) {
my $x = $tg_message->{reply_to_message}{from};
my $n;
if ($CONTEXT->{telegram_bot_id} eq $x->{id} && ($tg_message->{reply_to_message}{text} =~ m/\A ( <([^<>]+)> ) \s /x)) {
$n = $2;
}
$n //= $x->{username} // $x->{first_name};
$text .= $n . ": ";
}
$text .= $line;
if ($last_sent_text ne $text) {
$last_sent_text = $text;
$irc->write(PRIVMSG => $channel, ":$text\n", sub {});
sleep(1);
}
}
} else {
say "text-less message: " . Mojo::Util::dumper( $tg_message );
}
}
sub message_from_irc_to_tg {
state $last_sent_text = "";
my $chat_id = $CONTEXT->{telegram_group_chat_id} or return;
my $tg = $CONTEXT->{tg_bot} or return;
my ($irc_message) = @_;
my $text = $irc_message->{text};
my $from = $irc_message->{from};
if ($from =~ /^slackbot/) {
$from = "";
if ($text =~ s/\A ( <([a-zA-Z0-9_]+?)> ) \s //x) {
my $real_nick = $2;
$text = "<\x{24e2}${real_nick}> $text";
}
} elsif ($from =~ /^g0v-bridge/) {
$from = "";
if ($text =~ s/\A ( (.+?) \@ slack-legacy ) : \s //x) {
my $real_nick = $2;
$text = "<\x{24e2}${real_nick}> $text";
}
} else {
$from = "<$from> ";
}
my $tg_text = join('', $from, $text);
return if $last_sent_text eq $tg_text;
$last_sent_text = $tg_text;
$tg->api_request(
sendMessage => {
chat_id => $chat_id,
text => $tg_text,
}, sub {
my ($ua, $tx) = @_;
unless ($tx->success) {
say "sendMessage failed";
}
});
}
sub tg_get_updates {
return unless $CONTEXT->{tg_bot} && $CONTEXT->{telegram_group_chat_id};
state $max_update_id = -2;
$CONTEXT->{tg_bot}->api_request(
'getUpdates',
{ offset => ($max_update_id+1), timeout => 5 },
sub {
my ($ua, $tx) = @_;
if ($tx->success) {
my $res = $tx->res->json;
for (@{$res->{result}}) {
$max_update_id = max($max_update_id, $_->{update_id});
if ($CONTEXT->{telegram_group_chat_id} == $_->{message}{chat}{id}) {
message_from_tg_to_irc($_->{message});
} else {
say "Unknown chat_id: " . Mojo::Util::dumper($_);
}
}
} else {
say "getUpdates failed: " . Mojo::Util::dumper( $tx->error );
}
}
);
}
sub tg_init {
my ($token) = @_;
my $tgbot = WWW::Telegram::BotAPI->new( token => $token, async => 1 );
if ($tgbot->agent->can("inactivity_timeout")) {
$tgbot->agent->inactivity_timeout(180);
}
my $get_me_cb;
$get_me_cb = sub {
my ($ua, $tx) = @_;
if ($tx->success) {
my $r = $tx->res->json;
Mojo::Util::dumper(['getMe', $r]);
Mojo::IOLoop->recurring( 15, \&tg_get_updates );
} else {
Mojo::Util::dumper(['getMe Failed.', $tx->res->body]);
Mojo::IOLoop->timer( 5 => sub { $tgbot->api_request(getMe => $get_me_cb) });
}
};
Mojo::IOLoop->timer( 5 => sub { $tgbot->api_request(getMe => $get_me_cb) });
return $tgbot;
}
sub irc_init {
my ($nick, $server, $channel) = @_;
my $irc;
$irc = Mojo::IRC::UA->new(
nick => $nick,
user => $nick,
server => $server,
);
$irc->op_timeout(120);
$irc->register_default_event_handlers;
$irc->on(
irc_join => sub {
my($self, $message) = @_;
});
$irc->on(
irc_privmsg => sub {
my($self, $message) = @_;
my ($c, $text) = @{ $message->{params} };
return unless $c eq $channel;
my $from_nick = IRC::Utils::parse_user($message->{prefix});
message_from_irc_to_tg({ from => $from_nick, text => $text });
});
$irc->on(
irc_rpl_welcome => sub {
say "-- connected";
$irc->join_channel(
$channel,
sub {
my ($self, $err, $info) = @_;
say "-- join $channel -- topic - $info->{topic}";
}
);
});
$irc->on(error => sub {
my ($self, $message) = @_;
Mojo::IOLoop->timer( 10 => sub { $irc->connect(sub{}) } );
});
$irc->connect(sub {});
return $irc;
}
sub MAIN {
my (%args) = @_;
$CONTEXT->{irc_server} = $args{irc_server};
$CONTEXT->{irc_nickname} = $args{irc_nickname};
$CONTEXT->{irc_channel} = $args{irc_channel};
$CONTEXT->{telegram_group_chat_id} = $args{telegram_group_chat_id};
$CONTEXT->{telegram_bot_id} = substr($args{telegram_token}, 0, index($args{telegram_token}, ":"));
$CONTEXT->{tg_bot} = tg_init( $args{telegram_token} );
$CONTEXT->{irc_bot} = irc_init($args{irc_nickname}, $args{irc_server}, $args{irc_channel});
Mojo::IOLoop->start;
}
my %args;
GetOptions(
\%args,
"irc_nickname=s",
"irc_server=s",
"irc_channel=s",
"telegram_token=s",
"telegram_group_chat_id=s",
);
MAIN(%args);
| gugod/tgircbot | tgircbot.pl | Perl | cc0-1.0 | 6,163 |
#
# Copyright 2022 Centreon (http://www.centreon.com/)
#
# Centreon is a full-fledged industry-strength solution that meets
# the needs in IT infrastructure and application monitoring for
# service performance.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
#
package network::citrix::appacceleration::snmp::plugin;
use strict;
use warnings;
use base qw(centreon::plugins::script_snmp);
sub new {
my ($class, %options) = @_;
my $self = $class->SUPER::new(package => __PACKAGE__, %options);
bless $self, $class;
$self->{version} = '0.1';
%{$self->{modes}} = (
'cpu' => 'network::citrix::appacceleration::snmp::mode::cpu',
'list-serviceclass' => 'network::citrix::appacceleration::snmp::mode::listserviceclass',
'serviceclass-usage' => 'network::citrix::appacceleration::snmp::mode::serviceclassusage',
);
return $self;
}
1;
__END__
=head1 PLUGIN DESCRIPTION
Check Citrix Application Acceleration Module in SNMP (CloudBridge, Orbital, Repeater).
=cut
| centreon/centreon-plugins | network/citrix/appacceleration/snmp/plugin.pm | Perl | apache-2.0 | 1,547 |
package Bio::BioVeL::Service::NeXMLExtractor::CharSetWriter::nexus;
use strict;
use warnings;
use Bio::BioVeL::Service::NeXMLExtractor::CharSetWriter;
use base 'Bio::BioVeL::Service::NeXMLExtractor::CharSetWriter';
=over
=item write_charsets
Writes character set definitions to a NEXUS string. The syntax is expected to be like what
is used inside C<mrbayes> blocks and inside C<sets> blocks, i.e.:
charset <name> = <start coordinate>(-<end coordinate>)?(\<offset>)? ...;
That is, the definition starts with the C<charset> token, a name and an equals sign. Then,
one or more coordinate sets. Each coordinate set has a start coordinate, an optional end
coordinate (otherwise it's interpreted as a single site), and an optional offset statement,
e.g. for codon positions. Alternatively, instead of coordinates, names of other character
sets may be used. The statement ends with a semicolon.
=back
=cut
sub write_charsets {
my ( $self, $charsets ) = @_;
my $str = "#nexus\n";
$str .= "begin sets;\n";
my %h = %{$charsets};
foreach my $name (keys %h) {
$str .= "charset $name = ";
my $sets_ref = $h{$name};
my @sets = @{$sets_ref};
foreach my $set (@sets) {
$str .= $set->{"start"} == $set->{"end"} ? $set->{"start"} : $set->{"start"} . "-" . $set->{"end"};
my $offset = $set->{"offset"};
if ($offset > 1){
$str .= "\\" . $offset;
}
$str .= " ";
}
$str .= ";\n";
}
$str .= "end;\n";
return $str;
}
1;
| naturalis/biovel-nbc | lib/Bio/BioVeL/Service/NeXMLExtractor/CharSetWriter/nexus.pm | Perl | apache-2.0 | 1,741 |
?- pj_add_predicate(meta_data/2, 'org.projog.core.predicate.udp.PredicateMetaData').
p(a).
p(b(_)).
p(c(1)).
p(c(2)).
p(c(3)).
p(d) :- repeat(2).
p(e(X,X)) :- repeat(2).
p(f(1)).
p(f(_)).
p(f(2)).
p(g).
%?- meta_data(p(_), X)
% X=factory_class : org.projog.core.predicate.udp.StaticUserDefinedPredicateFactory
% X=factory_isRetryable : true
% X=factory_isAlwaysCutOnBacktrack : false
% X=actual_class : org.projog.core.predicate.udp.StaticUserDefinedPredicateFactory$NotIndexablePredicateFactory
% X=actual_isRetryable : true
% X=actual_isAlwaysCutOnBacktrack : false
% X=processed_class : org.projog.core.predicate.udp.StaticUserDefinedPredicateFactory$NotIndexablePredicateFactory
% X=processed_isRetryable : true
% X=processed_isAlwaysCutOnBacktrack : false
%?- p(X)
% X=a
% X=b(_)
% X=c(1)
% X=c(2)
% X=c(3)
% X=d
% X=d
% X=e(X, X)
% X=e(X, X)
% X=f(1)
% X=f(_)
% X=f(2)
% X=g
%?- meta_data(p(a), X)
% X=factory_class : org.projog.core.predicate.udp.StaticUserDefinedPredicateFactory
% X=factory_isRetryable : true
% X=factory_isAlwaysCutOnBacktrack : false
% X=actual_class : org.projog.core.predicate.udp.StaticUserDefinedPredicateFactory$NotIndexablePredicateFactory
% X=actual_isRetryable : true
% X=actual_isAlwaysCutOnBacktrack : false
% X=processed_class : org.projog.core.predicate.udp.SingleNonRetryableRulePredicateFactory
% X=processed_isRetryable : false
% X=processed_isAlwaysCutOnBacktrack : false
%TRUE p(a)
%?- meta_data(p(d), X)
% X=factory_class : org.projog.core.predicate.udp.StaticUserDefinedPredicateFactory
% X=factory_isRetryable : true
% X=factory_isAlwaysCutOnBacktrack : false
% X=actual_class : org.projog.core.predicate.udp.StaticUserDefinedPredicateFactory$NotIndexablePredicateFactory
% X=actual_isRetryable : true
% X=actual_isAlwaysCutOnBacktrack : false
% X=processed_class : org.projog.core.predicate.udp.SingleRetryableRulePredicateFactory
% X=processed_isRetryable : true
% X=processed_isAlwaysCutOnBacktrack : false
%?- p(d)
%YES
%YES
%?- meta_data(p(b(z)), X)
% X=factory_class : org.projog.core.predicate.udp.StaticUserDefinedPredicateFactory
% X=factory_isRetryable : true
% X=factory_isAlwaysCutOnBacktrack : false
% X=actual_class : org.projog.core.predicate.udp.StaticUserDefinedPredicateFactory$NotIndexablePredicateFactory
% X=actual_isRetryable : true
% X=actual_isAlwaysCutOnBacktrack : false
% X=processed_class : org.projog.core.predicate.udp.SingleNonRetryableRulePredicateFactory
% X=processed_isRetryable : false
% X=processed_isAlwaysCutOnBacktrack : false
%TRUE p(b(z))
%?- meta_data(p(c(_)), X)
% X=factory_class : org.projog.core.predicate.udp.StaticUserDefinedPredicateFactory
% X=factory_isRetryable : true
% X=factory_isAlwaysCutOnBacktrack : false
% X=actual_class : org.projog.core.predicate.udp.StaticUserDefinedPredicateFactory$NotIndexablePredicateFactory
% X=actual_isRetryable : true
% X=actual_isAlwaysCutOnBacktrack : false
% X=processed_class : org.projog.core.predicate.udp.StaticUserDefinedPredicateFactory$LinkedHashMapPredicateFactory
% X=processed_isRetryable : true
% X=processed_isAlwaysCutOnBacktrack : false
%?- p(c(X))
% X=1
% X=2
% X=3
%?- meta_data(p(e(1,1)), X)
% X=factory_class : org.projog.core.predicate.udp.StaticUserDefinedPredicateFactory
% X=factory_isRetryable : true
% X=factory_isAlwaysCutOnBacktrack : false
% X=actual_class : org.projog.core.predicate.udp.StaticUserDefinedPredicateFactory$NotIndexablePredicateFactory
% X=actual_isRetryable : true
% X=actual_isAlwaysCutOnBacktrack : false
% X=processed_class : org.projog.core.predicate.udp.SingleRetryableRulePredicateFactory
% X=processed_isRetryable : true
% X=processed_isAlwaysCutOnBacktrack : false
%?- p(e(1,1))
%YES
%YES
%?- meta_data(p(e(1,2)), X)
% X=factory_class : org.projog.core.predicate.udp.StaticUserDefinedPredicateFactory
% X=factory_isRetryable : true
% X=factory_isAlwaysCutOnBacktrack : false
% X=actual_class : org.projog.core.predicate.udp.StaticUserDefinedPredicateFactory$NotIndexablePredicateFactory
% X=actual_isRetryable : true
% X=actual_isAlwaysCutOnBacktrack : false
% X=processed_class : org.projog.core.predicate.udp.NeverSucceedsPredicateFactory
% X=processed_isRetryable : false
% X=processed_isAlwaysCutOnBacktrack : false
%FAIL p(e(1,2))
%?- meta_data(p(f(3)), X)
% X=factory_class : org.projog.core.predicate.udp.StaticUserDefinedPredicateFactory
% X=factory_isRetryable : true
% X=factory_isAlwaysCutOnBacktrack : false
% X=actual_class : org.projog.core.predicate.udp.StaticUserDefinedPredicateFactory$NotIndexablePredicateFactory
% X=actual_isRetryable : true
% X=actual_isAlwaysCutOnBacktrack : false
% X=processed_class : org.projog.core.predicate.udp.SingleNonRetryableRulePredicateFactory
% X=processed_isRetryable : false
% X=processed_isAlwaysCutOnBacktrack : false
%TRUE p(f(3))
%?- meta_data(p(f(_)), X)
% X=factory_class : org.projog.core.predicate.udp.StaticUserDefinedPredicateFactory
% X=factory_isRetryable : true
% X=factory_isAlwaysCutOnBacktrack : false
% X=actual_class : org.projog.core.predicate.udp.StaticUserDefinedPredicateFactory$NotIndexablePredicateFactory
% X=actual_isRetryable : true
% X=actual_isAlwaysCutOnBacktrack : false
% X=processed_class : org.projog.core.predicate.udp.StaticUserDefinedPredicateFactory$NotIndexablePredicateFactory
% X=processed_isRetryable : true
% X=processed_isAlwaysCutOnBacktrack : false
%?- p(f(X))
% X=1
% X=UNINSTANTIATED VARIABLE
% X=2
%?- meta_data(p(z), X)
% X=factory_class : org.projog.core.predicate.udp.StaticUserDefinedPredicateFactory
% X=factory_isRetryable : true
% X=factory_isAlwaysCutOnBacktrack : false
% X=actual_class : org.projog.core.predicate.udp.StaticUserDefinedPredicateFactory$NotIndexablePredicateFactory
% X=actual_isRetryable : true
% X=actual_isAlwaysCutOnBacktrack : false
% X=processed_class : org.projog.core.predicate.udp.NeverSucceedsPredicateFactory
% X=processed_isRetryable : false
% X=processed_isAlwaysCutOnBacktrack : false
%FAIL p(z)
| s-webber/projog | src/test/prolog/udp/predicate-meta-data/NotIndexablePredicateFactory.pl | Perl | apache-2.0 | 5,952 |
#
# 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 storage::dell::compellent::snmp::mode::components::cache;
use strict;
use warnings;
use storage::dell::compellent::snmp::mode::components::resources qw(%map_sc_status);
my $mapping = {
scCacheStatus => { oid => '.1.3.6.1.4.1.674.11000.2000.500.1.2.28.1.3', map => \%map_sc_status },
scCacheName => { oid => '.1.3.6.1.4.1.674.11000.2000.500.1.2.28.1.4' },
};
my $oid_scCacheEntry = '.1.3.6.1.4.1.674.11000.2000.500.1.2.28.1';
sub load {
my ($self) = @_;
push @{$self->{request}}, { oid => $oid_scCacheEntry, begin => $mapping->{scCacheStatus}->{oid}, end => $mapping->{scCacheName}->{oid} };
}
sub check {
my ($self) = @_;
$self->{output}->output_add(long_msg => "Checking caches");
$self->{components}->{cache} = {name => 'caches', total => 0, skip => 0};
return if ($self->check_filter(section => 'cache'));
foreach my $oid ($self->{snmp}->oid_lex_sort(keys %{$self->{results}->{$oid_scCacheEntry}})) {
next if ($oid !~ /^$mapping->{scCacheStatus}->{oid}\.(.*)$/);
my $instance = $1;
my $result = $self->{snmp}->map_instance(mapping => $mapping, results => $self->{results}->{$oid_scCacheEntry}, instance => $instance);
next if ($self->check_filter(section => 'cache', instance => $instance));
$self->{components}->{cache}->{total}++;
$self->{output}->output_add(long_msg => sprintf("cache '%s' status is '%s' [instance = %s]",
$result->{scCacheName}, $result->{scCacheStatus}, $instance,
));
my $exit = $self->get_severity(label => 'default', section => 'cache', value => $result->{scCacheStatus});
if (!$self->{output}->is_status(value => $exit, compare => 'ok', litteral => 1)) {
$self->{output}->output_add(severity => $exit,
short_msg => sprintf("Cache '%s' status is '%s'", $result->{scCacheName}, $result->{scCacheStatus}));
}
}
}
1; | wilfriedcomte/centreon-plugins | storage/dell/compellent/snmp/mode/components/cache.pm | Perl | apache-2.0 | 2,793 |
# 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.
package SupportingEvidenceInfo;
=pod
=head1 NAME
SupportingEvidenceInfo
=head1 SYNOPSIS
A module to identify supporting evidence associated with transcripts and
genes on the basis of both gene ids and evidence ids
=head1 DESCRIPTION
This module can be given an evidence id (either protein or cdna) or a gene
or transcript id then find either the gene ids which it supports of the
evidence which supports it
=head1 CONTACT
ensembl dev mailing list <http://lists.ensembl.org/mailman/listinfo/dev>
=head1 APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
=cut
use vars qw(@ISA $AUTOLOAD);
use strict;
use Bio::EnsEMBL::Utils::Exception qw(throw warning);
@ISA = qw( );
sub new{
my ($class, @args) = @_;
my $self = bless {},$class;
return $self;
}
=head2 Container methods
Arg [1] : SupportingEvidenceInfo
Arg [2] : value of variable
Function : container for specified variable. This pod refers to the
seven methods below, db, verbose, info, evidence_type, id_type
have_pfetch and primary_evidence. These are simple containers which do no
more than hold and return an given value
Returntype: value of variable
Exceptions: some throw if type is incorrect
Example : my $db = SupportingEvidenceInfo->db;
=cut
sub db{
my ($self, $db) = @_;
if($db){
if(!($db->isa('Bio::EnsEMBL::DBSQL::DBAdaptor'))){
throw("Must pass SupportingEvidenceInfo:db a DBAdaptor not a $db");
}
$self->{'db'} = $db;
}
return $self->{'db'};
}
sub verbose{
my ($self, $value) = @_;
if(defined($value)){
$self->{'verbose'} = $value;
}
return $self->{'verbose'};
}
sub info{
my ($self, $value) = @_;
if(defined($value)){
$self->{'info'} = $value;
}
return $self->{'info'};
}
sub evidence_type{
my ($self, $value) = @_;
if($value){
$self->{'evidence_type'} = $value;
}
return $self->{'evidence_type'} || 'protein_align_feature';
}
sub id_type{
my ($self, $value) = @_;
if($value){
$self->{'id_type'} = $value;
}
return $self->{'id_type'} || 'gene';
}
sub have_pfetch{
my ($self, $value) = @_;
if(defined($value)){
$self->{'have_pfetch'} = $value;
}
return $self->{'have_pfetch'};
}
sub primary_evidence{
my ($self, $value) = @_;
if(defined($value)){
$self->{'primary_evidence'} = $value;
}
return $self->{'primary_evidence'};
}
=head2 evidence_ids_from_feature_id
Arg [1] : SupportingEvidenceInfo
Arg [2] : int, transcript or gene dbID
Arg [3] : string, table name, gene or transcript
Arg [4] : string, evidence type dna_align_feature or protein_align_feature
Arg [5] : Bio::EnsEMBL::DBSQL::DBAdaptor
Function : find which evidence ids of the type specified are associated
with this dbID
Returntype: none
Exceptions: none
Example : $supportingevidenceinfo->(1);
=cut
sub evidence_ids_from_feature_id{
my ($self, $transcript_id, $id_type, $evidence_type, $primary, $db) = @_;
if(!$db){
$db = $self->db;
}
if(!$evidence_type){
$evidence_type = $self->evidence_type;
}
if(!$id_type){
$id_type = $self->id_type;
}
if(!$primary){
$primary = $self->primary_evidence;
}
my @protein_ids;
my $sql;
if($primary){
$sql = $self->primary_evidence_from_feature_id_sql($transcript_id,
$evidence_type,
$id_type);
}else{
$sql = $self->evidence_from_feature_id_sql($transcript_id,
$evidence_type,
$id_type);
}
print "SQL: ".$sql."\n" if($self->verbose);
my $sth = $db->dbc->prepare($sql);
$sth->execute();
while(my ($protein_id) = $sth->fetchrow){
print"Have protein id ".$protein_id."\n" if($self->verbose);
push(@protein_ids, $protein_id);
}
$self->fetch_descriptions(\@protein_ids);
}
=head2 feature_ids_from_evidence_id
Arg [1] : SupportingEvidenceInfo
Arg [2] : string, evidence identifier
Arg [3] : string, gene type
Arg [4] : string, table name, gene or transcript
Arg [5] : string, evidence type dna_align_feature or
protein_align_feature
Arg [6] : Bio::EnsEMBL::DBSQL::DBAdaptor
Function : get the dbIDs of any genes or transcripts which have this
as part of their supporting evidence
Returntype: none
Exceptions: none
Example : $supportingevidenceinfo->
feature_ids_from_evidence_id('Q8K1F0');
=cut
sub feature_ids_from_evidence_id{
my ($self, $evidence_id, $gene_type, $evidence_type, $id_type,
$primary, $db) = @_;
if(!$db){
$db = $self->db;
}
if(!$evidence_type){
$evidence_type = $self->evidence_type;
}
if(!$id_type){
$id_type = $self->id_type;
}
if(!$primary){
$primary = $self->primary_evidence;
}
my $sql;
if($primary){
$sql = $self->feature_id_from_primary_evidence_sql($evidence_id,
$evidence_type,
$id_type,
$gene_type);
}else{
$sql = $self->feature_id_from_evidence_sql($evidence_id,
$evidence_type,
$id_type,
$gene_type);
}
print "SQL:".$sql."\n" if($self->verbose);
my $sth = $db->dbc->prepare($sql);
$sth->execute();
while(my ($feature_id) = $sth->fetchrow){
if($self->info){
print $evidence_id." ";
my $adaptor = $self->get_adaptor($id_type, $db);
my $feature = $adaptor->fetch_by_dbID($feature_id);
$self->print_feature_info($feature);
}else{
print $evidence_id ." ".$feature_id."\n";
}
}
}
sub dbID_from_stable_id{
my ($self, $stable_id, $id_type, $db) = @_;
$db = $self->db if(!$db);
$id_type = $self->id_type if(!$id_type);
my $sql = "select ".$id_type."_id ".
"from ".$id_type."_stable_id ".
"where stable_id = ?";
print "SQL: $sql \n" if($self->verbose);
my $sth = $db->dbc->prepare($sql);
$sth->execute($stable_id);
my ($dbID) = $sth->fetchrow;
return $dbID;
}
=head2 fetch_descriptions
Arg [1] : SupportingEvidenceInfo
Arg [2] : Arrayref (array of ids for pfetch)
Function : fetch descriptions for given identifiers from pfetch
Returntype: none
Exceptions: throws if faileds to open or close the pmatch command
Example : $self->fetch_descriptions(\@protein_ids);
=cut
sub fetch_descriptions{
my ($self, $protein_ids) = @_;
ID:foreach my $id(@$protein_ids){
if($id =~ /(S+)-\1/){
$id = 1;
}
if($self->have_pfetch){
my $command = "pfetch -D ".$id."\n";
print $command."\n" if($self->verbose);
open(FH, $command." | ") or throw("failed to open ".$command);
LINE:while(<FH>){
if(/no\s+match/){
print $id." has no match\n";
next LINE;
}
print;
}
close(FH) or throw("Failed to close $command");
}else{
print $id."\n";
}
}
}
=head2 print_feature_info
Arg [1] : SupportingEvidenceInfo
Arg [2] : Bio::EnsEMBL::Feature
Function : prints location information about feature give
Returntype: none
Exceptions: none
Example : $self->print_feature_info($transcript);
=cut
sub print_feature_info{
my ($self, $feature) = @_;
throw("Must pass print_feature_info a feature") if(!$feature);
my $info_string = $feature->dbID." ";
$info_string .= $feature->stable_id if($feature->stable_id);
$info_string .= $feature->slice->seq_region_name." ".
$feature->slice->coord_system_name." ".$feature->start." ".
$feature->end." ".$feature->strand."\n";
print $info_string."\n";
}
=head2 get_adaptor
Arg [1] : SupportingEvidenceInfo
Arg [2] : string, id type gene or transcript
Arg [3] : Bio::EnsEMBL::DBSQL::DBAdaptor
Function : get an appropriate buisness adaptor for the features
wanted
Returntype: Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor
Exceptions: throws if not passed a recognised type
Example :
=cut
sub get_adaptor{
my ($self, $id_type, $db) = @_;
$db = $self->db if(!$db);
$id_type = $id_type if(!$id_type);
if($id_type eq 'gene'){
return $db->get_GeneAdaptor;
}elsif($id_type eq 'transcript'){
return $db->get_TranscriptAdaptor;
}
throw("Failed to get adaptor for feature type ".$id_type);
}
=head2 read_id_file
Arg [1] : SupportingEvidenceInfo
Arg [2] : string, filename
Function : read file to produce a list of ids, takes the first word
from each line
Returntype: arrayref
Exceptions: throws if fails to open or close file
Example : my $ids = SupportingEvidenceInfo->read_id_file($file)
=cut
sub read_id_file{
my ($self, $file) = @_;
open(FH, $file) or throw("Failed to open ".$file);
my @ids;
while(<FH>){
chomp;
my ($id) = split;
push(@ids, $id);
}
close(FH) or throw("Failed to close ".$file);
return \@ids;
}
#Methods to return the SQL
=head2 sql methods
Arg [1] : SupportingEvidenceInfo
Function : These methods all take arguments to be used to produce
an sql string to be used in order to fetch either evidence or feature
ids. What is different is if they fetch on the basis of primary evidence
associated with whole transcripts or all the evidence associated with each
exon
Returntype: string
Exceptions: none
Example :
=cut
sub primary_evidence_from_feature_id_sql{
my ($self, $feature_id, $evidence_type, $id_type) = @_;
my $sql = ("SELECT distinct(hit_name) ".
"FROM transcript, ".
"transcript_supporting_feature, ".
"$evidence_type ".
"WHERE transcript.".$id_type."_id = ".$feature_id." ".
"and transcript.transcript_id = ".
"transcript_supporting_feature.transcript_id ".
"and feature_type = '".$evidence_type."' ".
"and feature_id = ".$evidence_type."_id ");
return $sql;
}
sub evidence_from_feature_id_sql{
my ($self, $feature_id, $evidence_type, $id_type) = @_;
my $sql = ("select distinct(hit_name) ".
"from $evidence_type, supporting_feature, ".
"exon_transcript, exon, transcript ".
"where ".$evidence_type."_id = feature_id ".
"and feature_type = '$evidence_type'".
"and supporting_feature.exon_id = exon_transcript.exon_id ".
"and exon_transcript.transcript_id = ".
"transcript.transcript_id ".
"and transcript.".$id_type."_id = $feature_id");
return $sql;
}
sub feature_id_from_primary_evidence_sql{
my ($self, $evidence_id, $evidence_type, $id_type, $gene_type) = @_;
my $sql = ("SELECT distinct(transcript.".$id_type."_id) ".
"FROM transcript, transcript_supporting_feature, ".
"gene, $evidence_type ".
"WHERE transcript.gene_id = gene.gene_id ".
"and transcript.transcript_id = ".
"transcript_supporting_feature.transcript_id ".
"and feature_type = '$evidence_type' ".
"and feature_id = ".$evidence_type."_id ".
"and hit_name = '$evidence_id' ");
$sql .= "and biotype = '".$gene_type."' " if($gene_type);
return $sql;
}
sub feature_id_from_evidence_sql{
my ($self, $evidence_id, $evidence_type, $id_type, $gene_type) = @_;
my $sql = ("SELECT distinct(transcript.".$id_type."_id) ".
"FROM transcript, exon_transcript, supporting_feature, ".
"$evidence_type, gene ".
"WHERE hit_name = '$evidence_id' ".
"AND ".$evidence_type."_id = feature_id ".
"AND feature_type = '$evidence_type' ".
"AND supporting_feature.exon_id = exon_transcript.exon_id ".
"AND exon_transcript.transcript_id = ".
"transcript.transcript_id ".
"AND transcript.gene_id = gene.gene_id");
$sql .= " AND biotype = '".$gene_type."'" if($gene_type);
return $sql;
}
1;
| mn1/ensembl-analysis | scripts/buildchecks/SupportingEvidenceInfo.pm | Perl | apache-2.0 | 12,832 |
=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
package EnsEMBL::Users::Command::Account::Group::Delete;
### Command module to delete a group
### @author hr5
use strict;
use warnings;
use EnsEMBL::Users::Messages qw(MESSAGE_UNKNOWN_ERROR MESSAGE_GROUP_NOT_FOUND);
use base qw(EnsEMBL::Users::Command::Account);
sub csrf_safe_process {
my $self = shift;
my $object = $self->object;
my $hub = $self->hub;
my $user = $hub->user;
my $return_url;
if (my $group_id = $hub->param('id')) {
if (my $membership = $object->fetch_accessible_membership_for_user($user->rose_object, $group_id, {
'with_objects' => ['group', 'group.memberships', 'group.records'],
'query' => ['level' => 'administrator']
})) {
my $group = $membership->group;
# do we need to notify anyone?
my @curious_admins = map {$_->user_id ne $user->user_id && $_->notify_edit && $_->user || ()} @{$group->admin_memberships};
my $group_name = $group->name;
if ($group->delete('cascade' => 1)) {
$self->mailer->send_group_deletion_notification_email(\@curious_admins, $group_name);
$return_url = {'action' => 'Groups', 'function' => ''};
} else {
$return_url = {'action' => 'Groups', 'function' => 'View', 'id' => $group_id, 'err' => MESSAGE_UNKNOWN_ERROR};
}
}
}
return $self->ajax_redirect($hub->url($return_url || {'action' => 'Groups', 'function' => '', 'err' => MESSAGE_GROUP_NOT_FOUND}));
}
1;
| andrewyatz/public-plugins | users/modules/EnsEMBL/Users/Command/Account/Group/Delete.pm | Perl | apache-2.0 | 2,120 |
#!/usr/bin/env perl
use strict;
use warnings;
use File::Find;
use File::Copy;
use File::Remove 'remove';
use File::Spec;
my $DOWNLOAD_DIR='download';
my $EXTRACT_DIR='extract';
my $CATALYST_DIR= File::Spec->rel2abs('../root/static/lib');
-d $CATALYST_DIR || die "cannot find catalyst static directory";
my $JS_DIR = "$CATALYST_DIR/js";
my $CSS_DIR = "$CATALYST_DIR/css";
my $FONTS_DIR = "$CATALYST_DIR/fonts";
my $IMAGES_DIR = "$CATALYST_DIR/images";
sub get_filename {
my $url = shift;
$url =~ m|/([^/]+)$| and return $1;
die "don't know how to save url $url";
}
sub download_extract {
my $url = shift;
my $target = "$DOWNLOAD_DIR/".get_filename($url);
-f $target || download($url);
system("unzip", $target, "-d", $EXTRACT_DIR);
}
sub download {
my $url = shift;
my $filename = get_filename($url);
system ("curl", "-s", "-S", "-L", $url, "-o", "$DOWNLOAD_DIR/$filename");
}
sub install_file {
my $dest;
-f or return;
/\.js$/ and $dest = $JS_DIR;
/\.css$/ and $dest = $CSS_DIR;
/^glyphicons/ and $dest = $FONTS_DIR;
$dest or return;
copy($_, $dest) and print "$_ -> $dest\n" or die "cannot move $_ to $dest: $!";
}
mkdir $DOWNLOAD_DIR unless -d $DOWNLOAD_DIR;
-d $EXTRACT_DIR && remove(\1, $EXTRACT_DIR);
mkdir $EXTRACT_DIR;
download_extract("http://code.angularjs.org/1.2.9/angular-1.2.9.zip");
download_extract("https://github.com/twbs/bootstrap/releases/download/v3.1.1/bootstrap-3.1.1-dist.zip");
#provided by bootstrap
#download( "http://code.jquery.com/jquery-1.11.0.min.js");
#download( "http://code.jquery.com/jquery-1.11.0.js");
find( \&install_file, $EXTRACT_DIR );
| gmambro/nocview-poc | ext-libs/install.pl | Perl | apache-2.0 | 1,669 |
time(Goal,Time) :-
statistics(runtime,[Global1,_]),
call(Goal),
statistics(runtime,[Global2,_TimeSinceLastStat]),
Time is Global2 - Global1.
time(Goal) :-
time(Goal,Time),
print('Time for goal: '),print(Goal),
print(' is: '),print(Time), print(' ms'),nl.
add_new_time_log_entry(NameOfEntry,LogFile) :-
open_log(LogFile,Stream),
nl(Stream),
print(Stream,NameOfEntry),
close(Stream).
time_log(Goal,LogFile) :-
open_log(LogFile,Stream),
time(Goal,Time),
format(Stream,"\t",[]),
print(Stream,Time),
close(Stream).
open_log(LogFile,Stream) :-
(open(LogFile,append,Stream,[])
-> true
; open(LogFile,write,Stream,[])).
| leuschel/ecce | ecce_benchmarks/time.pl | Perl | apache-2.0 | 731 |
#!/usr/bin/perl -w
# This is an openssl-style command-line encrypter. *Please* don't use it
# except for testing, as your key will be exposed.
use strict;
use warnings;
use Crypt::Rijndael_PP_a;
use MIME::Base64;
my ($iv, $key)=map {pack("H*", $_)} @ARGV;
$/=undef;
my $ctext=<STDIN>;
print Crypt::Rijndael_PP_a::block_decrypt_CBC($iv,decode_base64($ctext),$key);
| jj101k/Crypt_Rijndael_PP_a | utility/decrypt.pl | Perl | bsd-2-clause | 371 |
#
# $Id: Tor.pm,v eff9afda3723 2015/01/04 12:34:23 gomor $
#
# network::tor Brik
#
package Metabrik::Network::Tor;
use strict;
use warnings;
use base qw(Metabrik::Client::Www);
sub brik_properties {
return {
revision => '$Revision: eff9afda3723 $',
tags => [ qw(unstable tor exitnodes) ],
attributes => {
uri => [ qw(uri) ],
},
# alternatives:
# https://www.dan.me.uk/torlist/
# https://check.torproject.org/exit-addresses
#
# https://www.dan.me.uk/torcheck?ip=2.100.184.78
# https://globe.torproject.org/
# https://atlas.torproject.org/
attributes_default => {
uri => 'http://torstatus.blutmagie.de/ip_list_exit.php/Tor_ip_list_EXIT.csv',
},
commands => {
exit_nodes_list => [ ],
},
};
}
sub exit_nodes_list {
my $self = shift;
my $get = $self->get or return $self->log->error('exit_nodes_list: get failed');
my $ip_list = $get->{body};
my @ip_list = split(/\n/, $ip_list);
my %ip_list = ();
for my $ip (@ip_list) {
$ip_list{$ip} = 1;
}
return {
as_list => \@ip_list,
as_hash => \%ip_list,
};
}
1;
__END__
=head1 NAME
Metabrik::Network::Tor - network::tor Brik
=head1 COPYRIGHT AND LICENSE
Copyright (c) 2014-2015, Patrice E<lt>GomoRE<gt> Auffret
You may distribute this module under the terms of The BSD 3-Clause License.
See LICENSE file in the source distribution archive.
=head1 AUTHOR
Patrice E<lt>GomoRE<gt> Auffret
=cut
| gitpan/Metabrik-Repository | lib/Metabrik/Network/Tor.pm | Perl | bsd-3-clause | 1,514 |
use strict;
use warnings;
use lib '../lib';
use MJ12::Remote::ApiService;
# check input.
my $script = __FILE__;
die "usage: $script privatekey accesstoken item1 item2 item3 (where item is a domain,subdomain or url)" unless scalar(@ARGV > 2);
my $endpoint = "http://enterprise.majesticseo.com/api_command";
# credentials.
my $private_key = shift @ARGV;
my $access_token = shift @ARGV;
# create query parameters.
my %params = (
'items' => scalar(@ARGV),
'datasource' => 'fresh',
);
for (my $i = 0; $i < scalar(@ARGV); $i++)
{
$params{'item'.$i} = $ARGV[$i];
}
my $api_service = new MJ12::Remote::ApiService('ApplicationId' => $private_key, 'Endpoint' => $endpoint);
my $response = $api_service->executeOpenAppRequest('AccessToken' => $access_token, 'CommandName' => 'GetIndexItemInfo', 'Params' => \%params);
# check the response code.
if($response->isOK())
{
# dump results table.
my $results = $response->tableForName('Name' => 'Results');
foreach my $row (@{$results->rowsAsArrayRef()})
{
my $item = $row->{'Item'};
print "\n<$item>\n";
# each row is a hashref.
foreach my $key (sort keys %{$row})
{
unless ($key eq 'Item')
{
my $value = $row->{$key};
print " $key ... $value\n";
}
}
}
if("http://developer.majesticseo.com/api_command" eq $endpoint)
{
print "\n\n***********************************************************" .
"*****************";
print "\n\nEndpoint: " . $endpoint;
print "\n\nThis program is hard-wired to the Developer API " .
"and hence the subset of data \nreturned will be substantially " .
"smaller than that which will be returned from \neither the " .
"Enterprise API or the Majestic SEO website.";
print "\n\nTo make this program use the Enterprise API, change " .
"the endpoint to: \nhttp://enterprise.majesticseo.com/api_command.";
print "\n\n***********************************************************" .
"*****************\n";
}
}
else
{
print "\n\nERROR MESSAGE:";
print "\n" . $response->errorMessage;
print "\n\n\n***********************************************************" .
"*****************";
print "\n\nDebugging Info:";
print "\n\n Endpoint: \t" . $endpoint;
print "\n OpenApp \"private key\": \t" . $private_key;
print "\n Access Token: \t" . $access_token;
if("http://enterprise.majesticseo.com/api_command" eq $endpoint)
{
print "\n\n Is this API Key valid for this Endpoint?";
print "\n\n This program is hard-wired to the Enterprise API.";
print "\n\n If you do not have access to the Enterprise API, " .
"change the endpoint to: \n http://developer.majesticseo.com/api_command.";
}
print "\n\n***********************************************************" .
"*****************\n";
}
=head1 LICENSE
Copyright 2015, Majestic-12 Ltd trading as Majestic
https://majestic.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:
* 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 Majestic-12 Ltd, its trademarks, nor any contributors
to the software 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 Majestic-12 Ltd 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
| MajesticSEO/Perl-API-Connector | scripts/openapp_get_index_item_info.pl | Perl | bsd-3-clause | 4,628 |
=head1 NAME
grid-matching - Executes occupancy grid matching techniques
=head1 SYNOPSIS
grid-matching --match --map1=I<grid1.simplemap> --map2=I<grid1.simplemap> [I<options>]
grid-matching --detect-test --map1=I<grid1.simplemap> [I<options>]
=head1 DESCRIPTION
B<grid-matching> is a command-line application which takes two maps as input and computes
a Sum-Of-Gaussians (SOG) density distribution for the 2D transformation between them, if
they are found to match.
=head1 OPTIONS
B<--match> Operation: match two maps
B<--detect-test> Operation: Quality of match with one map
B<--map1> arg Map #1 to align (*.simplemap)
B<--map2> arg Map #2 to align (*.simplemap)
B<--out> arg (=gridmatching_out.txt) Output file for the results
B<--config> arg Optional config. file with more params
B<--save-sog-3d> Save a 3D view of all the SOG modes
B<--save-sog-all> Save all the map overlaps
B<--noise-xy> arg (=0) In detect-test mode,std. noise in XY
B<--noise-phi> arg (=0) In detect-test mode,std. noise in PHI (deg)
B<--Ax> arg (=4) In detect-test mode, displacement in X
B<--Ay> arg (=2) In detect-test mode, displacement in Y
B<--Aphi> arg (=30) In detect-test mode, displ. in PHI (deg)
B<--verbose> verbose output
B<--nologo> skip the logo at startup
B<--help> produce help message
=head1 BUGS
Please report bugs at https://github.com/MRPT/mrpt/issues
=head1 SEE ALSO
The application wiki page at https://www.mrpt.org/Applications
=head1 AUTHORS
B<grid-matching> is part of the Mobile Robot Programming Toolkit (MRPT), and was originally
written by the MAPIR laboratory (University of Malaga).
This manual page was written by Jose Luis Blanco <joseluisblancoc@gmail.com>.
=head1 COPYRIGHT
This program is free software; you can redistribute it and/or modify it
under the terms of the BSD License.
On Debian GNU/Linux systems, the complete text of the BSD License can be
found in `/usr/share/common-licenses/BSD'.
=cut
| MRPT/mrpt | doc/man-pages/pod/grid-matching.pod | Perl | bsd-3-clause | 2,249 |
=head1 NAME
Fasta - Simple object for Fasta sequence
=head1 SYNOPSIS
my $seq=new Fasta( $hdr, $seq );
$seq->qc;
print $seq->output;
=head1 DESCRIPTION
Object for a single read sequence, with methods for basic manipulation and quality control.
=head1 METHODS
=over 5
=cut
package Fasta;
use constant {
CHARACTERS_PER_LINE => 80, # for formatting Fasta output
CLOSE_ENOUGH_TO_END => 6, # hits of adapters this close to end will result in trimming to be done to end
};
=item new $hdr $seq
Initialize new sequence object.
=cut
sub new {
my ($class,$hdr,$seq)=@_;
chomp $hdr;
chomp $seq;
die("Incomplete Fasta record: hdr=$hdr, seq=$seq\n") unless $hdr and $seq;
# INIT
my $this={
hdr=>$hdr, # complete header (e.g. ">A/1 description")
seq=>$seq # complete sequence without newlines
};
bless $this,$class;
$this->_parse_header;
return $this;
}
# DESTRUCTOR - closes file before going away
sub DESTROY {
my $this=shift;
close $this->{fh} if exists($this->{fh}) and defined($this->{fh});
}
sub _parse_header {
my $this=shift;
my $hdr=$this->{hdr};
$this->{id}=undef; # complete ID (e.g. "A/1#GATTACA"); always defined
$this->{base}=undef; # base ID only (e.g. "A"); always defined
$this->{pair}=undef; # pair ID only (e.g. "1"); only defined if paired
$this->{barcode}=undef; # barcode sequence (upper-case); only defined it barcoded
if ($hdr =~ /^>(\S+)#([aAtTcCgGnN]+)\/([12])/) { # barcoded, paired
$this->{base}=$1;
$this->{barcode}=uc($2);
$this->{pair}=$3;
} elsif ($hdr =~ /^>(\S+)\/([12])#([aAtTcCgGnN]+)/) { # barcoded, paired
$this->{base}=$1;
$this->{pair}=$2;
$this->{barcode}=uc($3);
} elsif ($hdr =~ /^>(\S+)\/([12])/) { # paired
$this->{base}=$1;
$this->{pair}=$2;
} elsif ($hdr =~ /^>(\S+)#([aAtTcCgGnN]+)/) { # barcoded, unpaired
$this->{base}=$1;
$this->{barcode}=uc($2);
} elsif ($hdr =~ /^>(\S+)/) { # unpaired or other
$this->{base}=$1;
} else {
die "Unable to parse header: $hdr\n";
}
$this->{id}=$this->{base};
$this->{id} .= "/".$this->{pair} if $this->{pair};
$this->{id} .= "#".$this->{barcode} if $this->{barcode}
}
=item header ($new_hdr)
Returns the object's header line. You can also use this method to give the sequence a new header.
=cut
sub header {
my ($this,$new_hdr)=@_;
if (defined($new_hdr) and $new_hdr) {
$new_hdr = $1 if $new_hdr =~ /^[>@](.+)$/;
$new_hdr = '>'.$new_hdr unless $new_hdr =~ /^>/;
$this->_parse_header($new_hdr);
}
return '>'.$this->{id};
}
=item id
Returns the object's ID, which is the sequence's unique identifier without comments which may be present in the header.
It cannot be changed directly, but will be updated whenever the header, base, or pair is changed.
=cut
sub id { return shift->{id} }
=item base
If the read is paired, returns it's base ID (same for both members of pair); returns undefined if not paired.
Providing the optional argument will change the base (and the id and header).
=cut
sub base {
my ($this,$base)=@_;
if ($base) {
$this->{id}=$this->{base}=$base;
$this->{id} .= "/".$this->{pair} if $this->{pair};
$this->{id} .= "#".$this->{barcode} if $this->{barcode}
}
return $this->{base};
}
=item barcode
If the read contains an Illumina molecular barcode ID, it will be returned; otherwise returns undef.
Supplying an optional argument will set the barcode.
=cut
sub barcode {
my ($this,$barcode)=@_;
if ($barcode) {
$this->{barcode}=$barcode;
$this->{id}=$this->{base}=$base;
$this->{id} .= "/".$this->{pair} if $this->{pair};
$this->{id} .= "#".$barcode;
$this->_recreate_header;
}
return $this->{barcode};
}
=item pair
Returns the read's ord in the pair; undef otherwise. It may be changed by supplying the optional extra argument.
To clear the pairing information, pass it an empty string, not NULL.
=cut
sub pair {
my ($this,$pair)=@_;
if (defined($pair)) {
if ($pair) {
$this->{pair}=$pair;
$this->{id}=$this->{base}=$base;
$this->{id} .= "/".$pair;
$this->{id} .= "#".$this->{barcode} if $this->{barcode}
} else {
# delete pairing information (e.g. singleton)
$this->{pair}=undef;
$this->{id}=$this->{base}=$base;
$this->{id} .= "#".$this->{barcode} if $this->{barcode}
}
}
return $this->{pair};
}
=item seq ($new_seq)
Returns the read's complete sequence, without newlines. Optional argument changes it.
=cut
sub seq {
my ($this,$new_seq)=@_;
if ($new_seq) {
chomp $new_seq;
$this->{seq}=$new_seq;
}
return $this->{seq};
}
=item revcomp
Reverse-complements a sequence.
=cut
sub revcomp {
my $this=shift;
return unless $this->{seq};
$this->{seq} =~ tr/ATCGatcg/TAGCtagc/;
my @seq=reverse split(//, $this->{seq});
$this->{seq}=join('', @seq);
}
=item output
Returns a multiline string of the sequence in Fasta format. Returns no output if sequence is empty.
=cut
sub output {
my $this=shift;
return '' unless $this->{seq}; # will be empty if failed QC
return $this->{hdr}."\n"._format($this->{seq});
}
# PRIVATE METHOD TO ADD NEWLINE CHARACTERS
sub _format {
my $old=shift;
return '' unless $old;
return $old unless CHARACTERS_PER_LINE;
my $new='';
while (length($old)> CHARACTERS_PER_LINE) {
$new .= substr($old,0, CHARACTERS_PER_LINE)."\n";
$old = substr($old, CHARACTERS_PER_LINE);
}
$new .= $old."\n";
return $new;
}
###############################################################################
## QC METHODS
=back
=head2 QC Methods
=over 5
=item qc $winsize $meanq $minlen $maxn
To perform minimum length filtering, and filtering reads with too many Ns.
=cut
sub qc {
my ($this, $minlen, $maxn)=@_;
$this->trim_terminal_Ns;
$this->length_filter($minlen);
$this->N_filter($maxn);
}
=item trim_terminal_Ns
Discard uninformative Ns from the ends of the sequence.
=cut
sub trim_terminal_Ns {
my $this=shift;
if ($this->seq =~ /^(N+)(.*)$/) {
$this->seq($2);
}
if ($this->seq =~ /^(.*)N+$/) {
$this->seq($1);
}
}
=item length_filter
If the sequence is shorter than the minimum length, the sequence string is emptied so they will not be
returned by the output method. Returns true if sequence was filtered.
=cut
sub length_filter {
my ($this,$minlen)=@_;
my $len=length($this->{seq});
if ( !defined($minlen) or $len >= $minlen) {
return 0;
} else {
$this->{seq}='';
return 1;
}
}
=item N_filter
If the sequence contains more than the allowed number of Ns, the sequence string is emptied.
Returns true if sequence was filtered.
=cut
sub N_filter {
my ($this,$maxn)=@_;
return 1 unless defined($maxn);
# COUNT NUMBER OF 'N' BASES IN TRIMMED SEQ
my $tmpseq=$this->{seq};
my $n= $tmpseq=~ s/N//gi;
if ($n <= $maxn) {
return 0;
} else {
# FAIL
$this->{seq}='';
return 1;
}
}
=item low_complexity_filter $pct_len
If the sequence is >= $pct_len mono- or di-nucleotide repeats, clears the sequence string and returns true.
=cut
sub low_complexity_filter {
my ($this,$pct_len)=@_;
my $seq=$this->{seq};
$seq =~ s/\n//g;
my $len = length($seq);
my $filter=0;
foreach my $nn (qw/AA TT CC GG CA GT CT GA AT CG/) {
my $n = $seq =~ s/$nn/$nn/g;
if ($n >= $pct_len/200*$len) {
$filter = 1;
last;
}
}
if ($filter) {
$this->{seq}='';
}
return $filter;
}
#=item trim
#
#Given start and end coordinates of adapter/primer sequence, trims sequence string and returns final length.
#
#=cut
#
#sub trim {
# my ($this, $start, $end)=@_;
# return unless defined($start) and defined($end);
# ($start,$end)=($end,$start) if $end<$start;
# my $len=length($this->{seq});
# #print STDERR "- trim read, ", $this->id, " ($len bp) from $start-$end\n"; # DEBUG
#
# if ($start <= CLOSE_ENOUGH_TO_END and $len - $end <= CLOSE_ENOUGH_TO_END ) {
# # fail read
# $this->{seq}='';
# } elsif ($start <= CLOSE_ENOUGH_TO_END ) {
# # trim left
# $this->{seq}=substr($this->{seq},$end);
# } elsif ($len - $end <= CLOSE_ENOUGH_TO_END ) {
# # trim right
# $this->{seq}=substr($this->{seq},0,$start);
# }
# return length($this->{seq});
# #print STDERR "\t+ length after trimming is ", length($this->{seq})," bp\n"; # DEBUG
#}
=back
=head1 BUGS AND LIMITATIONS
No support for paired reads.
=head1 COPYRIGHT
Copyright (c) 2010 U.S. Department of Energy Joint Genome Institute
All right reserved. This program is free software; you can redistribute it
and/or modify it under the same terms as Perl itself.
=head1 AUTHOR
Edward Kirton <ESKirton@LBL.gov>
=cut
###############################################################################
## FASTADB OBJECT
=head1 NAME
FastaDb - Simple object for handling Fasta files
=head1 SYNOPSIS
# simple script to QC reads (outputs to stdout)
use FastaDb;
my $file=shift or die("Infile required\n");
my $fastaFile = new FastaFile($file);
while (my $fasta=$fastaFile->next_seq) {
$fasta->qc; # see Fasta package for details
print $fasta->output; # no output if read failed QC
}
=head1 DESCRIPTION
This module provides an iterator for Fasta files, plus basic QC functions
=head1 METHODS
=over 5
=cut
package FastaDb;
use IO::File;
use File::Basename;
use Cwd;
sub new {
my ($class,$file)=@_;
# VALIDATE
die("Fasta file required\n") unless $file;
# USE FULL PATH
my $cwd=getcwd.'/';
my ($base,$dir,$suffix)=fileparse($file, qr/\.[^.]*/);
$dir=$cwd if $dir eq './';
$file="$dir$base$suffix";
# INIT
my $this = { file => $file, next_header => undef };
$this->{fh} = new IO::File("<$file") or die("Unable to open Fasta file, $file: $!\n");
bless $this,$class;
return $this;
}
=item file ($new_file)
Returns the Fasta db complete path. You may also use this method to open a new file for reading.
=cut
sub file {
my ($this,$new_file)=@_;
if ($new_file) {
$this->close_file;
$this->{fh}=new IO::File('<'.$new_file) or die("Unable to open Fasta file, $new_file: $!\n");
}
return $this->{file};
}
=item next_seq
An iterator for the fasta database; returns a single sequence as multiline text.
=cut
sub next_seq {
my $this=shift;
return undef unless exists($this->{fh}) and defined($this->{fh});
# INIT VARS
my $fh = $this->{fh};
my $hdr=undef;
my $seq='';
if (defined($this->{next_header})) {
$hdr=$this->{next_header};
$this->{next_header}=undef;
} else {
# GET FIRST HEADER
while (<$fh>) {
chomp;
if (/^>\S+/) {
$hdr=$_;
last;
} elsif (/^#/ or ! $_) {
next;
} else {
die("Invalid input file format; choked on line: $_\n");
}
}
}
unless (defined($hdr)) {
$this->close_file;
return undef;
}
# GET SEQ
while (<$fh>) {
chomp;
if (/^>\S+/) {
$this->{next_header}=$_;
last;
} elsif($_) {
$seq .= $_;
}
}
# CHECK IF END OF FILE OR PART
if ( !defined($this->{next_header}) ) {
$this->close_file;
}
# RETURN ONE FASTA SEQ
return new Fasta($hdr,$seq);
}
=item close_file
This will close the file and delete the file handle. Normally this is called by the iterator upon reaching the end
of the file, so this method only needs to be called if you wish to close the file prematurely.
=cut
sub close_file {
my $this=shift;
return unless exists($this->{fh}) and defined($this->{fh});
close $this->{fh};
delete $this->{fh};
}
1;
=back
=head1 BUGS AND LIMITATIONS
No support for paired reads.
=head1 COPYRIGHT
Copyright (c) 2010 U.S. Department of Energy Joint Genome Institute
All right reserved. This program is free software; you can redistribute it
and/or modify it under the same terms as Perl itself.
=head1 AUTHOR
Edward Kirton <ESKirton@LBL.gov>
=cut
| xibalbanus/PIA2 | pia/FastaDb.pm | Perl | mit | 12,583 |
package Games::Lacuna::Client::Buildings::SpacePort;
use 5.0080000;
use strict;
use warnings;
use Carp 'croak';
use Games::Lacuna::Client;
use Games::Lacuna::Client::Buildings;
our @ISA = qw(Games::Lacuna::Client::Buildings);
sub api_methods {
return {
view => { default_args => [qw(session_id building_id)] },
view_all_ships => { default_args => [qw(session_id building_id)] },
view_foreign_ships => { default_args => [qw(session_id building_id)] },
get_ships_for => { default_args => [qw(session_id)] },
send_ship => { default_args => [qw(session_id)] },
send_fleet => { default_args => [qw(session_id)] },
recall_ship => { default_args => [qw(session_id building_id)] },
recall_all => { default_args => [qw(session_id building_id)] },
name_ship => { default_args => [qw(session_id building_id)] },
scuttle_ship => { default_args => [qw(session_id building_id)] },
view_ships_travelling => { default_args => [qw(session_id building_id)] },
view_ships_orbiting => { default_args => [qw(session_id building_id)] },
prepare_send_spies => { default_args => [qw(session_id)] },
send_spies => { default_args => [qw(session_id)] },
prepare_fetch_spies => { default_args => [qw(session_id)] },
fetch_spies => { default_args => [qw(session_id)] },
view_battle_logs => { default_args => [qw(session_id building_id)] },
};
}
__PACKAGE__->init();
1;
__END__
=head1 NAME
Games::Lacuna::Client::Buildings::SpacePort - The Space Port building
=head1 SYNOPSIS
use Games::Lacuna::Client;
=head1 DESCRIPTION
=head1 AUTHOR
Steffen Mueller, E<lt>smueller@cpan.orgE<gt>
=head1 COPYRIGHT AND LICENSE
Copyright (C) 2010 by Steffen Mueller
This library is free software; you can redistribute it and/or modify
it under the same terms as Perl itself, either Perl version 5.10.0 or,
at your option, any later version of Perl 5 you may have available.
=cut
| RedOrion/Vasari-TLEUtil | lib/Games/Lacuna/Client/Buildings/SpacePort.pm | Perl | mit | 2,088 |
# <@LICENSE>
# 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.
# </@LICENSE>
# ---------------------------------------------------------------------------
# So, what's the difference between a trusted and untrusted Received header?
# Basically, relays we *know* are trustworthy are 'trusted', all others after
# the last one of those are 'untrusted'.
#
# We determine trust by detecting if they are inside the network ranges
# specified in 'trusted_networks'. There is also an inference algorithm
# which determines other trusted relays without user configuration.
#
# There's another type of Received header: the semi-trusted one. This is the
# header added by *our* MX, at the boundary of trust; we can trust the IP
# address (and possibly rDNS) in this header, but that's about it; HELO name is
# untrustworthy. We just use this internally for now.
#
# Finally, there's also 'internal_networks'. These are the networks that you
# control; your MXes should be included. This way, if you specify a wide range
# of trusted hosts, a mail that is relayed from a dynamic IP address via a
# 'trusted' host will not hit RCVD_IN_DYNABLOCK.
# ---------------------------------------------------------------------------
use strict; # make Test::Perl::Critic happy
package Mail::SpamAssassin::Message::Metadata::Received; 1;
package Mail::SpamAssassin::Message::Metadata;
use strict;
use warnings;
# use bytes;
use re 'taint';
use Mail::SpamAssassin::Dns;
use Mail::SpamAssassin::PerMsgStatus;
use Mail::SpamAssassin::Constants qw(:ip);
my $IP_ADDRESS = IP_ADDRESS;
my $IP_PRIVATE = IP_PRIVATE;
my $LOCALHOST = LOCALHOST;
# ---------------------------------------------------------------------------
sub parse_received_headers {
my ($self, $pms, $msg) = @_;
# a caller may assert that a message is coming from inside or from an
# authenticated roaming users; this info may not be available in mail
# header section, e.g. in case of nonstandard authentication mechanisms
my $originating; # boolean
if (exists $msg->{suppl_attrib}->{originating}) {
$originating = $msg->{suppl_attrib}->{originating} || 0;
dbg("metadata: set originating from suppl_attrib: %s", $originating);
}
$self->{relays_trusted} = [ ];
$self->{num_relays_trusted} = 0;
$self->{relays_trusted_str} = '';
$self->{relays_untrusted} = [ ];
$self->{num_relays_untrusted} = 0;
$self->{relays_untrusted_str} = '';
$self->{relays_internal} = [ ];
$self->{num_relays_internal} = 0;
$self->{relays_internal_str} = '';
$self->{relays_external} = [ ];
$self->{num_relays_external} = 0;
$self->{relays_external_str} = '';
$self->{num_relays_unparseable} = 0;
$self->{last_trusted_relay_index} = -1; # last counting from the top,
$self->{last_internal_relay_index} = -1; # first in time
$self->{allow_mailfetch_markers} = 1; # This needs to be set for the
# first Received: header
# now figure out what relays are trusted...
my $trusted = $pms->{main}->{conf}->{trusted_networks};
my $internal = $pms->{main}->{conf}->{internal_networks};
my $msa = $pms->{main}->{conf}->{msa_networks};
my $did_user_specify_trust = $pms->{main}->{conf}->{trusted_networks_configured};
my $did_user_specify_internal = $pms->{main}->{conf}->{internal_networks_configured};
my $in_trusted = 1;
my $in_internal = 1;
my $found_msa = 0;
unless ($did_user_specify_trust && $did_user_specify_internal) {
if (!$did_user_specify_trust && !$did_user_specify_internal) {
dbg('config: trusted_networks are not configured; it is recommended '.
'that you configure trusted_networks manually');
} elsif (!$did_user_specify_internal) {
# use 'trusted' for 'internal'; compatibility with SpamAssassin 2.60
$internal = $trusted;
dbg('config: internal_networks not configured, using trusted_networks '.
'configuration for internal_networks; if you really want '.
'internal_networks to only contain the required 127/8 add '.
"'internal_networks !0/0' to your configuration");
} else {
# use 'internal' for 'trusted'; I don't know why we let people define
# internal without trusted, but we do... and we rely on trusted being set
$trusted = $internal;
dbg('config: trusted_networks not configured, using internal_networks '.
'configuration for trusted_networks');
}
}
my @hdrs = $msg->get_header('Received');
# Now add the single line headers like X-Originating-IP. (bug 5680)
# we convert them into synthetic "Received" headers so we can share
# code below.
foreach my $header (@{$pms->{main}->{conf}->{originating_ip_headers}}) {
my $str = $msg->get_header($header);
next unless ($str && $str =~ m/($IP_ADDRESS)/);
push @hdrs, "from X-Originating-IP: $1\n";
}
foreach my $line ( @hdrs ) {
# qmail-scanner support hack: we may have had one of these set from the
# previous (read: more recent) Received header. if so, add it on to this
# header's set, since that's the handover it was describing.
my $qms_env_from;
if ($self->{qmail_scanner_env_from}) {
$qms_env_from = $self->{qmail_scanner_env_from};
delete $self->{qmail_scanner_env_from};
}
$line =~ s/\n[ \t]+/ /gs;
my $relay = $self->parse_received_line ($line);
if (!defined $relay) {
dbg("received-header: unparseable: $line");
$self->{num_relays_unparseable}++;
}
# undefined or 0 means there's no result, so goto the next header
unless ($relay) {
$self->{last_trusted_relay_index}++ if $in_trusted;
$self->{last_internal_relay_index}++ if $in_internal;
next;
}
# hack for qmail-scanner, as described above; add in the saved
# metadata
if ($qms_env_from) {
$relay->{envfrom} = $qms_env_from;
$self->make_relay_as_string($relay);
}
# relay status only changes when we're still in the trusted portion of the
# relays and we haven't yet found an MSA
if ($in_trusted && !$found_msa) {
unless ($did_user_specify_trust || $did_user_specify_internal) {
# OK, infer the trusted/untrusted handover, we don't have real info
my $inferred_as_trusted = 0;
# if the 'from' IP addr is in a reserved net range, it's not on
# the public internet.
if ($relay->{ip_private}) {
dbg("received-header: 'from' ".$relay->{ip}." has private IP");
$inferred_as_trusted = 1;
}
# if we find authentication tokens in the received header we can extend
# the trust boundary to that host
if ($relay->{auth}) {
dbg("received-header: authentication method ".$relay->{auth});
$inferred_as_trusted = 1;
}
# if the user didn't specify any trusted/internal config, everything
# we assume as trusted is also internal, just like we'd do if they
# specified trusted but not any internal networks or vice versa
if (!$inferred_as_trusted) {
dbg("received-header: do not trust any hosts from here on");
$in_trusted = 0;
$in_internal = 0;
}
} else {
# trusted_networks matches?
if (!$relay->{auth} && !$trusted->contains_ip($relay->{ip})) {
if (!$originating) {
$in_trusted = 0; # break the trust chain
} else { # caller asserts a msg was submitted from inside or auth'd
$found_msa = 1; # let's assume the previous hop was actually
# an MSA, and propagate trust from here on
dbg('received-header: originating, '.
'%s and remaining relays will be considered trusted%s',
$relay->{ip}, !$in_internal ? '' : ', but no longer internal');
}
$in_internal = 0; # if it's not trusted it's not internal
} else {
# internal_networks matches?
if ($in_internal && !$relay->{auth} && !$internal->contains_ip($relay->{ip})) {
$in_internal = 0;
}
# msa_networks matches?
if ($msa->contains_ip($relay->{ip})) {
dbg('received-header: found MSA relay, remaining relays will be'.
' considered trusted: '.($in_trusted ? 'yes' : 'no').
' internal: '.($in_internal ? 'yes' : 'no'));
$found_msa = 1;
$relay->{msa} = 1;
}
}
}
}
dbg("received-header: relay ".$relay->{ip}.
" trusted? ".($in_trusted ? "yes" : "no").
" internal? ".($in_internal ? "yes" : "no").
" msa? ".($relay->{msa} ? "yes" : "no"));
$relay->{internal} = $in_internal;
$relay->{msa} ||= 0;
# be sure to mark up the as_string version for users too
$relay->{as_string} =~ s/ intl=\d / intl=$relay->{internal} /;
$relay->{as_string} =~ s/ msa=\d / msa=$relay->{msa} /;
if ($in_trusted) {
push (@{$self->{relays_trusted}}, $relay);
$self->{allow_mailfetch_markers} = 1;
$self->{last_trusted_relay_index}++;
} else {
push (@{$self->{relays_untrusted}}, $relay);
$self->{allow_mailfetch_markers} = 0;
}
if ($in_internal) {
push (@{$self->{relays_internal}}, $relay);
$self->{last_internal_relay_index}++;
} else {
push (@{$self->{relays_external}}, $relay);
}
}
$self->{relays_trusted_str} = join(' ', map { $_->{as_string} }
@{$self->{relays_trusted}});
$self->{relays_untrusted_str} = join(' ', map { $_->{as_string} }
@{$self->{relays_untrusted}});
$self->{relays_internal_str} = join(' ', map { $_->{as_string} }
@{$self->{relays_internal}});
$self->{relays_external_str} = join(' ', map { $_->{as_string} }
@{$self->{relays_external}});
# OK, we've now split the relay list into trusted and untrusted.
# add the stringified representation to the message object, so Bayes
# and rules can use it. Note that rule_tests.t does not impl put_metadata,
# so protect against that here. These will not appear in the final
# message; they're just used internally.
if ($self->{msg}->can ("delete_header")) {
$self->{msg}->delete_header ("X-Spam-Relays-Trusted");
$self->{msg}->delete_header ("X-Spam-Relays-Untrusted");
$self->{msg}->delete_header ("X-Spam-Relays-Internal");
$self->{msg}->delete_header ("X-Spam-Relays-External");
if ($self->{msg}->can ("put_metadata")) {
$self->{msg}->put_metadata ("X-Spam-Relays-Trusted",
$self->{relays_trusted_str});
$self->{msg}->put_metadata ("X-Spam-Relays-Untrusted",
$self->{relays_untrusted_str});
$self->{msg}->put_metadata ("X-Spam-Relays-Internal",
$self->{relays_internal_str});
$self->{msg}->put_metadata ("X-Spam-Relays-External",
$self->{relays_external_str});
}
}
# be helpful; save some cumbersome typing
$self->{num_relays_trusted} = scalar (@{$self->{relays_trusted}});
$self->{num_relays_untrusted} = scalar (@{$self->{relays_untrusted}});
$self->{num_relays_internal} = scalar (@{$self->{relays_internal}});
$self->{num_relays_external} = scalar (@{$self->{relays_external}});
dbg("metadata: X-Spam-Relays-Trusted: ".$self->{relays_trusted_str});
dbg("metadata: X-Spam-Relays-Untrusted: ".$self->{relays_untrusted_str});
dbg("metadata: X-Spam-Relays-Internal: ".$self->{relays_internal_str});
dbg("metadata: X-Spam-Relays-External: ".$self->{relays_external_str});
}
# ---------------------------------------------------------------------------
# returns undef if the header just couldn't be parsed
# returns 0 if the header was specifically skipped
# returns a hash of information if the header is parsed, including:
# ip => $ip,
# by => $by,
# helo => $helo,
# id => $id,
# ident => $ident,
# envfrom => $envfrom,
# lc_by => (lc $by),
# lc_helo => (lc $helo),
# auth => $auth
#
sub parse_received_line {
my ($self) = shift;
local ($_) = shift;
local ($1,$2,$3,$4,$5,$6);
s/\s+/ /g;
s/^ //;
s/ $//;
# get rid of invalid semicolon at the end of the header
1 while s/\s?;$//;
my $ip = '';
my $helo = '';
my $rdns = '';
my $by = '';
my $id = '';
my $ident = '';
my $envfrom = undef;
my $mta_looked_up_dns = 0;
my $auth = '';
# ---------------------------------------------------------------------------
# We care about lines starting with from. all of the others are ignorable:
# Bug 4943: give /^(from/ a chance to be parsed
#
# (qmail 27981 invoked by uid 225); 14 Mar 2003 07:24:34 -0000
# (qmail 84907 invoked from network); 13 Feb 2003 20:59:28 -0000
# (ofmipd 208.31.42.38); 17 Mar 2003 04:09:01 -0000
# by faerber.muc.de (OpenXP/32 v3.9.4 (Win32) alpha @ 2003-03-07-1751d); 07 Mar 2003 22:10:29 +0000
# by x.x.org (bulk_mailer v1.13); Wed, 26 Mar 2003 20:44:41 -0600
# by SPIDERMAN with Internet Mail Service (5.5.2653.19) id <19AF8VY2>; Tue, 25 Mar 2003 11:58:27 -0500
# by oak.ein.cz (Postfix, from userid 1002) id DABBD1BED3; Thu, 13 Feb 2003 14:02:21 +0100 (CET)
# OTM-MIX(otm-mix00) id k5N1aDtp040896; Fri, 23 Jun 2006 10:36:14 +0900 (JST)
# at Infodrom Oldenburg (/\##/\ Smail-3.2.0.102 1998-Aug-2 #2) from infodrom.org by finlandia.Infodrom.North.DE via smail from stdin id <m1FglM8-000okjC@finlandia.Infodrom.North.DE> for debian-security-announce@lists.debian.org; Thu, 18 May 2006 18:28:08 +0200 (CEST)
# with ECARTIS (v1.0.0; list bind-announce); Fri, 18 Aug 2006 07:19:58 +0000 (UTC)
# Received: Message by Barricade wilhelm.eyp.ee with ESMTP id h1I7hGU06122 for <spamassassin-talk@lists.sourceforge.net>; Tue, 18 Feb 2003 09:43:16 +0200
return 0 if (!/^\(?from /i);
# from www-data by wwwmail.documenta.de (Exim 4.50) with local for <example@vandinter.org> id 1GFbZc-0006QV-L8; Tue, 22 Aug 2006 21:06:04 +0200
# from server.yourhostingaccount.com with local for example@vandinter.org id 1GDtdl-0002GU-QE (8710); Thu, 17 Aug 2006 21:59:17 -0400
return 0 if /\bwith local for\b/;
# Received: from virtual-access.org by bolero.conactive.com ; Thu, 20 Feb 2003 23:32:58 +0100
# Received: FROM ca-ex-bridge1.nai.com BY scwsout1.nai.com ; Fri Feb 07 10:18:12 2003 -0800
# but not: Received: from [86.122.158.69] by mta2.iomartmail.com; Thu, 2 Aug 2007 21:50:04 -0200
if (/^from (\S+) by [^\s;]+ ?;/i && $1 !~ /^\[[\d.]+\]$/) { return 0; }
# ---------------------------------------------------------------------------
# Let's get rid of the date at the end
# ; Tue, 23 May 2006 13:06:35 -0400
s/[\s;]+(?:(?:Mon|T(?:ue|hu)|Wed|Fri|S(?:at|un)), )?\d+ (?:J(?:an|u[nl])|Feb|Ma[ry]|A(?:pr|ug)|Sep|Oct|Nov|Dec) \d+ \d+:\d+(?::\d+)? \S+$//;
# from av0001.technodiva.com (localhost [127.0.0.1])by localhost.technodiva.com (Postfix) with ESMTP id 846CF2117for <proftp-user@lists.sourceforge.net>; Mon, 7 Aug 2006 17:48:07 +0200 (MEST)
s/\)by /) by /;
# ---------------------------------------------------------------------------
# OK -- given knowledge of most Received header formats,
# break them down. We have to do something like this, because
# some MTAs will swap position of rdns and helo -- so we can't
# simply use simplistic regexps.
# try to catch unique message identifier
if (/ id <?([^\s<>;]{3,})/) {
$id = $1;
}
if (/\bhelo=([-A-Za-z0-9\.\^+_&:=?!@%*\$\\\/]+)(?:[^-A-Za-z0-9\.\^+_&:=?!@%*\$\\\/]|$)/) {
$helo = $1;
}
elsif (/\b(?:HELO|EHLO) ([-A-Za-z0-9\.\^+_&:=?!@%*\$\\\/]+)(?:[^-A-Za-z0-9\.\^+_&:=?!@%*\$\\\/]|$)/) {
$helo = $1;
}
if (/ by (\S+)(?:[^-A-Za-z0-9\;\.]|$)/) { $by = $1; }
# ---------------------------------------------------------------------------
# try to catch authenticated message identifier
#
# with ESMTPA, ESMTPSA, LMTPA, LMTPSA should cover RFC 3848 compliant MTAs,
# UTF8SMTPA and UTF8LMTPA are covered by RFC 4954 and RFC 6531,
# with ASMTP (Authenticated SMTP) is used by Earthlink, Exim 4.34, and others
# with HTTP should only be authenticated webmail sessions
# with HTTPU is used by Communigate Pro with Pronto! webmail interface
# with HTTPS is used by Horde adjusts the Received header to say "HTTPS" when
# a connection is made over HTTPS
# IANA registry: https://www.iana.org/assignments/mail-parameters/mail-parameters.xhtml
if (/ by / && / with ((?:ES|L|UTF8S|UTF8L)MTPS?A|ASMTP|HTTP[SU]?)(?: |;|$)/i) {
$auth = $1;
}
# GMail should use ESMTPSA to indicate that it is in fact authenticated,
# but doesn't.
elsif (/ by mx\.google\.com with ESMTPS id [a-z0-9]{1,4}sm[0-9]{2,9}[a-z]{3}\.[0-9]{1,3}\.[0-9]{4}\.(?:[0-6][0-9]\.){4}[0-6][0-9]/ && /\(version=([^ ]+) cipher=([^\)]+)\)/ ) {
$auth = 'GMail - transport=' . $1 . ' cipher=' . $2;
}
# Courier v0.47 and possibly others
elsif (/^from .*?(?:\]\)|\)\]) \(AUTH: (LOGIN|PLAIN|DIGEST-MD5|CRAM-MD5) \S+(?:, .*?)?\) by /) {
$auth = $1;
}
# Sendmail, MDaemon, some webmail servers, and others
elsif (/authenticated/ && /^from .*?(?:\](?: \([^)]*\))?\)|\)\]) .*?\(.*?authenticated.*?\).*? by/) {
$auth = 'Sendmail';
}
# workaround for GMX, which authenticates users but does not indicate it properly - # SMTP version
elsif (/from \S* \((?:HELO|EHLO) (\S*)\) \[(${IP_ADDRESS})\] by (mail\.gmx\.(?:net|com)) \([^\)]+\) with ((?:ESMTP|SMTP))/) {
$auth = "GMX ($4 / $3)";
}
# Critical Path Messaging Server
elsif (/ \(authenticated as / && /\) by .+ \(\d{1,2}\.\d\.\d{3}(?:\.\d{1,3})?\) \(authenticated as .+\) id /) {
$auth = 'CriticalPath';
}
# Postfix 2.3 and later with "smtpd_sasl_authenticated_header yes"
# Normally $1 is "Postfix", but could be changed with mail_name (Bug 5646)
elsif (/\) \(Authenticated sender: \S+\) by \S+ \(([^\)]+)\) with /) {
$auth = $1 eq 'Postfix' ? $1 : "Postfix ($1)";
}
# Communigate Pro - Bug 6495 adds HTTP as possible transmission method
# Bug 7277: XIMSS used by Pronto and other custom apps, IMAP supports XMIT extension
elsif (/CommuniGate Pro (HTTP|SMTP|XIMSS|IMAP)/ && / \(account /) {
$auth = 'Communigate';
}
# Microsoft Exchange (complete with syntax error)
elsif (/ with Microsoft Exchange Server HTTP-DAV\b/) {
$auth = 'HTTP-DAV';
}
# froufrou mailers like United Internet use a '(via HTTP)' comment, Bug 7101
elsif (/ by / && / \(via (HTTP.?)\)(?: |;|$)/i) {
$auth = $1;
}
# ---------------------------------------------------------------------------
if (s/^from //) {
# try to catch enveloper senders
if (/(?:return-path:? |envelope-(?:sender|from)[ =])(\S+)\b/i) {
$envfrom = $1;
}
# from 142.169.110.122 (SquirrelMail authenticated user synapse) by
# mail.nomis80.org with HTTP; Sat, 3 Apr 2004 10:33:43 -0500 (EST)
# Expanded to NaSMail Bug 6783
if (/ \((?:SquirrelMail|NaSMail) authenticated user /) {
#REVERTING bug 3236 and implementing re: bug 6549
if (/(${IP_ADDRESS})\b(?![.-]).{10,80}by (\S+) with HTTP/) {
$ip = $1; $by = $2; goto enough;
}
}
# AOL WebMail headers
if (/aol\.com/ && /with HTTP \(WebMailUI\)/) {
# Received: from 82.135.198.129 by FWM-M18.sysops.aol.com (64.12.168.82) with HTTP (WebMailUI); Tue, 19 Jun 2007 11:16:54 -0400
if(/(${IP_ADDRESS}) by (\S+) \(${IP_ADDRESS}\) with HTTP \(WebMailUI\)/) {
$ip = $1; $by = $2; goto enough;
}
}
# catch MS-ish headers here
if (/ SMTPSVC/) {
# MS servers using this fmt do not lookup the rDNS.
# Received: from inet-vrs-05.redmond.corp.microsoft.com ([157.54.6.157])
# by INET-IMC-05.redmond.corp.microsoft.com with Microsoft
# SMTPSVC(5.0.2195.6624); Thu, 6 Mar 2003 12:02:35 -0800
# Received: from 0 ([61.31.135.91]) by bass.bass.com.eg with Microsoft
# SMTPSVC(5.0.2195.6713); Tue, 21 Sep 2004 08:59:06 +0300
# Received: from 0 ([61.31.138.57] RDNS failed) by nccdi.com with
# Microsoft SMTPSVC(6.0.3790.0); Thu, 23 Sep 2004 08:51:06 -0700
# Received: from tthompson ([217.35.105.172] unverified) by
# mail.neosinteractive.com with Microsoft SMTPSVC(5.0.2195.5329);
# Tue, 11 Mar 2003 13:23:01 +0000
# Received: from ([172.16.1.78]) by email2.codeworksonline.com with Microsoft SMTPSVC(5.0.2195.6713); Wed, 6 Sep 2006 21:14:29 -0400
if (/^(\S*) \(\[(${IP_ADDRESS})\][^\)]{0,40}\) by (\S+) with Microsoft SMTPSVC/) {
$helo = $1; $ip = $2; $by = $3; goto enough;
}
# Received: from mail pickup service by mail1.insuranceiq.com with
# Microsoft SMTPSVC; Thu, 13 Feb 2003 19:05:39 -0500
if (/^mail pickup service by (\S+) with Microsoft SMTPSVC$/) {
return 0;
}
}
# Microsoft SMTP Server
elsif (/ with (?:Microsoft SMTP Server|mapi id) (?:\([^\)]+\) )?\d+\.\d+\.\d+\.\d+(?:$| )/) {
# Received: from EXC-DAG-02.global.net (10.45.252.152) by EXC-DAG-02.global.net
# (10.45.252.152) with Microsoft SMTP Server (version=TLS1_2,
# cipher=TLS_ECDHE_RSA_WITH_AES_128_GCM_SHA256) id 15.1.1261.35;
# Mon, 29 Oct 2018 11:17:19 +0100
# Received: from AM5PR0402MB2836.eurprd04.prod.outlook.com
# ([fe80::19bd:c588:dd17:5226]) by AM5PR0402MB2836.eurprd04.prod.outlook.com
# ([fe80::19bd:c588:dd17:5226%6]) with mapi id 15.20.1943.023;
# Wed, 5 Jun 2019 10:17:08 +0000
if (/^(\S+) \(\[?(${IP_ADDRESS})(?:%[A-Z0-9._~-]*)?\]?\) by (\S+) /) {
$helo = $1; $ip = $2; $by = $3; $id = ''; goto enough;
}
}
elsif (/\[XMail /) { # bug 3791, bug 4053
# Received: from list.brainbuzz.com (63.146.189.86:23198) by mx1.yourtech.net with [XMail 1.20 ESMTP Server] id <S72E> for <jason@ellingson.org.spamassassin.org> from <bounce-cscommunity-11965901@list.cramsession.com.spamassassin.org>; Sat, 18 Sep 2004 23:17:54 -0500
# Received: from list.brainbuzz.com (63.146.189.86:23198) by mx1.yourtech.net (209.32.147.34:25) with [XMail 1.20 ESMTP Server] id <S72E> for <jason@ellingson.org.spamassassin.org> from <bounce-cscommunity-11965901@list.cramsession.com.spamassassin.org>; Sat, 18 Sep 2004 23:17:54 -0500
if (/^(\S+) \((\[?${IP_ADDRESS}\]?)(?::\d+)\) by (\S+)(?: \(\S+\))? with \[XMail/)
{
$helo = $1; $ip = $2; $by = $3;
/ id <(\S+)>/ and $id = $1;
/ from <(\S+)>/ and $envfrom = $1;
goto enough;
}
}
# from ([10.225.209.19:33672]) by ecelerity-va-1 (ecelerity HEAD) with SMTP id EE/20-30863-33CE1054; Fri, 08 Sep 2006 18:18:27 -0400
# from ([127.0.0.1:32923]) by bm1-21.ed10.com (ecelerity 2.1.1ea r(11031M)) with ECSTREAM id 8B/57-16227-3764EB44 for <example@vandinter.org>; Wed, 19 Jul 2006 10:49:23 -0400
# from ([192.168.1.151:49601] helo=dev1.democracyinaction.org) by m12.prod.democracyinaction.com (ecelerity 2.1.1.3 r(11743)) with ESMTP id 52/92-02454-89FBA054 for <example@vandinter.org>; Fri, 15 Sep 2006 10:58:32 -0400
elsif (/\(ecelerity\b/) {
if (/^\(\[(${IP_ADDRESS}):\d+\] helo=(\S+)\) by (\S+) /) {
$ip = $1; $helo = $2; $by = $3;
goto enough;
}
if (/^\S+ \(\[(${IP_ADDRESS}):\d+\]\) by (\S+) /) {
$ip = $1; $by = $2;
goto enough;
}
}
elsif (/Exim/) {
# one of the HUGE number of Exim formats :(
# This must be scriptable. (update: it is. cf bug 3950, 3582)
# mss 2004-09-27: See <http://www.exim.org/exim-html-4.40/doc/html/spec_14.html#IX1315>
# from root (helo=candygram.thunk.org) by thunker.thunk.org with local-esmtps (tls_cipher TLS-1.0:RSA_AES_256_CBC_SHA:32) (Exim 4.50 #1 (Debian)) id 1FwHqR-0008Bw-OG; Fri, 30 Jun 2006 08:11:35 -0400
# from root (helo=localhost) by broadcast.iac.iafrica.com with local-bsmtp (Exim 4.30; FreeBSD) id 1GN22d-0000xp-2K for example@vandinter.org; Tue, 12 Sep 2006 08:46:43 +0200
# from smarter (helo=localhost) by mx1-out.lists.smarterliving.com with local-bsmtp (Exim 4.24) id 1GIRA2-0007IZ-4n for example@vandinter.org; Wed, 30 Aug 2006 10:35:22 -0400
# Received: from andrew by trinity.supernews.net with local (Exim 4.12) id 18xeL6-000Dn1-00; Tue, 25 Mar 2003 02:39:00 +0000
if (/\bwith local(?:-\S+)? /) { return 0; }
# Received: from [61.174.163.26] (helo=host) by sc8-sf-list1.sourceforge.net with smtp (Exim 3.31-VA-mm2 #1 (Debian)) id 18t2z0-0001NX-00 for <razor-users@lists.sourceforge.net>; Wed, 12 Mar 2003 01:57:10 -0800
# Received: from [218.19.142.229] (helo=hotmail.com ident=yiuhyotp) by yzordderrex with smtp (Exim 3.35 #1 (Debian)) id 194BE5-0005Zh-00; Sat, 12 Apr 2003 03:58:53 +0100
if (/^\[(${IP_ADDRESS})\] \((.*?)\) by (\S+) /) {
$ip = $1; my $sub = $2; $by = $3;
$sub =~ s/helo=(\S+)// and $helo = $1;
$sub =~ s/ident=(\S*)// and $ident = $1;
goto enough;
}
# Received: from sc8-sf-list1-b.sourceforge.net ([10.3.1.13] helo=sc8-sf-list1.sourceforge.net) by sc8-sf-list2.sourceforge.net with esmtp (Exim 3.31-VA-mm2 #1 (Debian)) id 18t301-0007Bh-00; Wed, 12 Mar 2003 01:58:13 -0800
# Received: from dsl092-072-213.bos1.dsl.speakeasy.net ([66.92.72.213] helo=blazing.arsecandle.org) by sc8-sf-list1.sourceforge.net with esmtp (Cipher TLSv1:DES-CBC3-SHA:168) (Exim 3.31-VA-mm2 #1 (Debian)) id 18lyuU-0007TI-00 for <SpamAssassin-talk@lists.sourceforge.net>; Thu, 20 Feb 2003 14:11:18 -0800
# Received: from eclectic.kluge.net ([66.92.69.221] ident=[W9VcNxE2vKxgWHD05PJbLzIHSxcmZQ/O]) by sc8-sf-list1.sourceforge.net with esmtp (Cipher TLSv1:DES-CBC3-SHA:168) (Exim 3.31-VA-mm2 #1 (Debian)) id 18m0hT-00031I-00 for <spamassassin-talk@lists.sourceforge.net>; Thu, 20 Feb 2003 16:06:00 -0800
# Received: from mail.ssccbelen.edu.pe ([216.244.149.154]) by yzordderrex
# with esmtp (Exim 3.35 #1 (Debian)) id 18tqiz-000702-00 for
# <jm@example.com>; Fri, 14 Mar 2003 15:03:57 +0000
# Received: from server040.webpack.hosteurope.de ([80.237.130.48]:52313)
# by vps832469583.serverpool.info with esmtps
# (TLS-1.0:DHE_RSA_3DES_EDE_CBC_SHA:24) (Exim 4.50) id 1GzVLs-0002Oz-7b...
if (/^(\S+) \(\[(${IP_ADDRESS})\](.*?)\) by (\S+) /) {
$rdns=$1; $ip = $2; my $sub = $3; $by = $4;
$helo=$rdns; # default, apparently: bug 5112
$sub =~ s/helo=(\S+)// and $helo = $1;
$sub =~ s/ident=(\S*)// and $ident = $1;
goto enough;
}
# Received: from boggle.ihug.co.nz [203.109.252.209] by grunt6.ihug.co.nz
# with esmtp (Exim 3.35 #1 (Debian)) id 18SWRe-0006X6-00; Sun, 29 Dec
# 2002 18:57:06 +1300
if (/^(\S+) \[(${IP_ADDRESS})\](:\d+)? by (\S+) /) {
$rdns= $1; $ip = $2; $helo = $1; $by = $4; goto enough;
}
# attempt to deal with other odd Exim formats; just match little bits
# of the header.
# Received: from helene8.i.pinwand.net (helene.cats.ms) [10.0.8.6.13219]
# (mail) by lisbeth.i.pinwand.net with esmtp (Exim 3.35 #1 (Debian)) id
# 1CO5y7-0001vC-00; Sun, 31 Oct 2004 04:01:23 +0100
if (/^(\S+) /) {
$rdns= $1; # assume this is the rDNS, not HELO. is this appropriate?
}
if (/ \((\S+)\) /) {
$helo = $1;
}
if (/ \[(${IP_ADDRESS})(?:\.\d+)?\] /) {
$ip = $1;
}
if (/by (\S+) /) {
$by = $1;
# now, if we have a "by" and an IP, that's enough for most uses;
# we have to make do with that.
if ($ip) { goto enough; }
}
# else it's probably forged. fall through
}
elsif (/ \(Postfix\) with/) {
# Received: from localhost (unknown [127.0.0.1])
# by cabbage.jmason.org (Postfix) with ESMTP id A96E18BD97
# for <jm@localhost>; Thu, 13 Mar 2003 15:23:15 -0500 (EST)
if ( /^(\S+) \((\S+) \[(${IP_ADDRESS})\]\) by (\S+) / ) {
$mta_looked_up_dns = 1;
$helo = $1; $rdns = $2; $ip = $3; $by = $4;
if ($rdns eq 'unknown') { $rdns = ''; }
goto enough;
}
# Received: from 207.8.214.3 (unknown[211.94.164.65])
# by puzzle.pobox.com (Postfix) with SMTP id 9029AFB732;
# Sat, 8 Nov 2003 17:57:46 -0500 (EST)
# (Pobox.com version: reported in bug 2745)
if ( /^(\S+) \((\S+)\[(${IP_ADDRESS})\]\) by (\S+) / ) {
$mta_looked_up_dns = 1;
$helo = $1; $rdns = $2; $ip = $3; $by = $4;
if ($rdns eq 'unknown') { $rdns = ''; }
goto enough;
}
}
elsif (/\(Scalix SMTP Relay/) {
# from DPLAPTOP ( 72.242.176.162) by mail.puryear-it.com (Scalix SMTP Relay 10.0.1.3) via ESMTP; Fri, 23 Jun 2006 16:39:47 -0500 (CDT)
if (/^(\S+) \( ?(${IP_ADDRESS})\) by (\S+)/) {
$helo = $1; $ip = $2; $by = $3; goto enough;
}
}
elsif (/ \(Lotus Domino /) {
# it seems Domino never records the rDNS: bug 5926
if (/^(\S+) \(\[(${IP_ADDRESS})\]\) by (\S+) \(Lotus/) {
$mta_looked_up_dns = 0;
$helo = $1; $ip = $2; $by = $3; goto enough;
}
}
# Received: from 217.137.58.28 ([217.137.58.28])
# by webmail.ukonline.net (IMP) with HTTP
# for <anarchyintheuk@localhost>; Sun, 11 Apr 2004 00:31:07 +0100
if (/\bwith HTTP\b/ && # more efficient split up this way
/^(${IP_ADDRESS}) \(\[${IP_ADDRESS}\]\) by (\S+)/)
{
# some smarty-pants decided to fake a numeric HELO for HTTP
# no rDNS for this format?
$ip = $1; $by = $2; goto enough;
}
# MiB: 2003/11/29 Some qmail-ldap headers may be misinterpreted as sendmail-headers
# resulting in a messed-up interpretation. We have to skip sendmail tests
# if we find evidence that this is a qmail-ldap header.
#
unless (/ by \S+ \(qmail-\S+\) with /) {
#
# sendmail:
# Received: from mail1.insuranceiq.com (host66.insuranceiq.com [65.217.159.66] (may be forged)) by dogma.slashnull.org (8.11.6/8.11.6) with ESMTP id h2F0c2x31856 for <jm@jmason.org>; Sat, 15 Mar 2003 00:38:03 GMT
# Received: from BAY0-HMR08.adinternal.hotmail.com (bay0-hmr08.bay0.hotmail.com [65.54.241.207]) by dogma.slashnull.org (8.11.6/8.11.6) with ESMTP id h2DBpvs24047 for <webmaster@efi.ie>; Thu, 13 Mar 2003 11:51:57 GMT
# Received: from ran-out.mx.develooper.com (IDENT:qmailr@one.develooper.com [64.81.84.115]) by dogma.slashnull.org (8.11.6/8.11.6) with SMTP id h381Vvf19860 for <jm-cpan@jmason.org>; Tue, 8 Apr 2003 02:31:57 +0100
# from rev.net (natpool62.rev.net [63.148.93.62] (may be forged)) (authenticated) by mail.rev.net (8.11.4/8.11.4) with ESMTP id h0KKa7d32306 for <spamassassin-talk@lists.sourceforge.net>
#
if (/^(\S+) \((\S+) \[(${IP_ADDRESS})\].*\) by (\S+) \(/) {
$mta_looked_up_dns = 1;
$helo = $1; $rdns = $2; $ip = $3; $by = $4;
$rdns =~ s/^IDENT:([^\@]*)\@// and $ident = $1; # remove IDENT lookups
$rdns =~ s/^([^\@]*)\@// and $ident = $1; # remove IDENT lookups
goto enough;
}
}
# ---------------------------------------------------------------------------
## OK, AT THIS POINT FORMATS GET A BIT NON-STANDARD
# Received: from ns.elcanto.co.kr (66.161.246.58 [66.161.246.58]) by
# mail.ssccbelen.edu.pe with SMTP (Microsoft Exchange Internet Mail Service
# Version 5.5.1960.3) id G69TW478; Thu, 13 Mar 2003 14:01:10 -0500
if (/^(\S+) \((\S+) \[(${IP_ADDRESS})\]\) by (\S+) with \S+ \(/) {
$mta_looked_up_dns = 1;
$rdns = $2; $ip = $3; $helo = $1; $by = $4; goto enough;
}
# from mail2.detr.gsi.gov.uk ([51.64.35.18] helo=ahvfw.dtlr.gsi.gov.uk) by mail4.gsi.gov.uk with smtp id 190K1R-0000me-00 for spamassassin-talk-admin@lists.sourceforge.net; Tue, 01 Apr 2003 12:33:46 +0100
if (/^(\S+) \(\[(${IP_ADDRESS})\] helo=(\S+)\) by (\S+) with /) {
$rdns = $1; $ip = $2; $helo = $3; $by = $4;
goto enough;
}
# from 12-211-5-69.client.attbi.com (<unknown.domain>[12.211.5.69]) by rwcrmhc53.attbi.com (rwcrmhc53) with SMTP id <2002112823351305300akl1ue>; Thu, 28 Nov 2002 23:35:13 +0000
if (/^(\S+) \(<unknown\S*>\[(${IP_ADDRESS})\]\) by (\S+) /) {
$helo = $1; $ip = $2; $by = $3;
goto enough;
}
# from attbi.com (h000502e08144.ne.client2.attbi.com[24.128.27.103]) by rwcrmhc53.attbi.com (rwcrmhc53) with SMTP id <20030222193438053008f7tee>; Sat, 22 Feb 2003 19:34:39 +0000
if (/^(\S+) \((\S+\.\S+)\[(${IP_ADDRESS})\]\) by (\S+) /) {
$mta_looked_up_dns = 1;
$helo = $1; $rdns = $2; $ip = $3; $by = $4;
goto enough;
}
# Received: from 4wtgRl (kgbxn@[211.244.147.115]) by dogma.slashnull.org (8.11.6/8.11.6) with SMTP id h8BBsUJ18848; Thu, 11 Sep 2003 12:54:31 +0100
if (/^(\S+) \((\S*)\@\[(${IP_ADDRESS})\].*\) by (\S+) \(/) {
$mta_looked_up_dns = 1; # this one does. there just wasn't one
$helo = $1; $ip = $3; $by = $4;
$ident = $2;
goto enough;
}
# Received: from 213.123.174.21 by lw11fd.law11.hotmail.msn.com with HTTP;
# Wed, 24 Jul 2002 16:36:44 GMT
if (/by (\S+\.hotmail\.msn\.com) /) {
$by = $1;
/^(${IP_ADDRESS}) / and $ip = $1;
goto enough;
}
# Received: from x71-x56-x24-5.webspeed.dk (HELO niels) (69.96.3.15) by la.mx.develooper.com (qpsmtpd/0.27-dev) with SMTP; Fri, 02 Jan 2004 19:26:52 -0800
# Received: from sc8-sf-sshgate.sourceforge.net (HELO sc8-sf-netmisc.sourceforge.net) (66.35.250.220) by la.mx.develooper.com (qpsmtpd/0.27-dev) with ESMTP; Fri, 02 Jan 2004 14:44:41 -0800
# Received: from mx10.topofferz.net (HELO ) (69.6.60.10) by blazing.arsecandle.org with SMTP; 3 Mar 2004 20:34:38 -0000
if (/^(\S+) \((?:HELO|EHLO) (\S*)\) \((${IP_ADDRESS})\) by (\S+) \(qpsmtpd\/\S+\) with (?:ESMTP|SMTP)/) {
$rdns = $1; $helo = $2; $ip = $3; $by = $4; goto enough;
}
# Received: from mail-backend.DDDD.com (LHLO mail-backend.DDDD.com) (10.2.2.20) by mail-backend.DDDD.com with LMTP; Thu, 18 Jun 2015 16:50:56 -0700 (PDT)
if (/^(\S+) \(LHLO (\S*)\) \((${IP_ADDRESS})\) by (\S+) with LMTP/) {
$rdns = $1; $helo = $2; $ip = $3; $by = $4; goto enough;
}
# from dslb-082-083-045-064.pools.arcor-ip.net (EHLO homepc) [82.83.45.64] by mail.gmx.net (mp010) with SMTP; 03 Feb 2007 13:13:47 +0100
if (/^(\S+) \((?:HELO|EHLO) (\S*)\) \[(${IP_ADDRESS})\] by (\S+) \([^\)]+\) with (?:ESMTP|SMTP)/) {
$rdns = $1; $helo = $2; $ip = $3; $by = $4; goto enough;
}
# MiB (Michel Bouissou, 2003/11/16)
# Moved some tests up because they might match on qmail tests, where this
# is not qmail
#
# Received: from imo-m01.mx.aol.com ([64.12.136.4]) by eagle.glenraven.com
# via smtpd (for [198.85.87.98]) with SMTP; Wed, 08 Oct 2003 16:25:37 -0400
if (/^(\S+) \(\[(${IP_ADDRESS})\]\) by (\S+) via smtpd \(for \S+\) with SMTP\(/) {
$helo = $1; $ip = $2; $by = $3; goto enough;
}
# Try to match most of various qmail possibilities
#
# General format:
# Received: from postfix3-2.free.fr (HELO machine.domain.com) (foobar@213.228.0.169) by totor.bouissou.net with SMTP; 14 Nov 2003 08:05:50 -0000
#
# "from (remote.rDNS|unknown)" is always there
# "(HELO machine.domain.com)" is there only if HELO differs from remote rDNS.
# HELO may be "" -- ie no string. "HELO" may also be "EHLO". HELO string
# may be an IP in fmt [1.2.3.4] -- do not strip [ and ], they are important.
# "foobar@" is remote IDENT info, specified only if ident given by remote
# Remote IP always appears between (parentheses), with or without IDENT@
# "by local.system.domain.com" always appears
#
# Protocol can be different from "SMTP", i.e. "RC4-SHA encrypted SMTP" or "QMQP"
# qmail's reported protocol shouldn't be "ESMTP", so by allowing only "with (.* )(SMTP|QMQP)"
# we should avoid matching on some sendmailish Received: lines that reports remote IP
# between ([218.0.185.24]) like qmail-ldap does, but use "with ESMTP".
#
# Normally, qmail-smtpd remote IP isn't between square brackets [], but some versions of
# qmail-ldap seem to add square brackets around remote IP. These versions of qmail-ldap
# use a longer format that also states the (envelope-sender <sender@domain>) and the
# qmail-ldap version. Example:
# Received: from unknown (HELO terpsichore.farfalle.com) (jdavid@[216.254.40.70]) (envelope-sender <jdavid@farfalle.com>) by mail13.speakeasy.net (qmail-ldap-1.03) with SMTP for <jm@jmason.org>; 12 Feb 2003 18:23:19 -0000
#
# Some others of the numerous qmail patches out there can also add variants of their own
#
# Received: from 211.245.85.228 (EHLO ) (211.245.85.228) by mta232.mail.scd.yahoo.com with SMTP; Sun, 25 Jan 2004 00:24:37 -0800
#
# bug 4813: make sure that the line doesn't have " id " after the
# protocol since that's a sendmail line and not qmail ...
if (/^\S+( \((?:HELO|EHLO) \S*\))? \((\S+\@)?\[?${IP_ADDRESS}\]?\)( \(envelope-sender <\S+>\))? by \S+( \(.+\))* with (.* )?(SMTP|QMQP)(?! id )/ ) {
if (/^(\S+) \((?:HELO|EHLO) ([^ \(\)]*)\) \((\S*)\@\[?(${IP_ADDRESS})\]?\)( \(envelope-sender <\S+>\))? by (\S+)/) {
$rdns = $1; $helo = $2; $ident = $3; $ip = $4; $by = $6;
}
elsif (/^(\S+) \((?:HELO|EHLO) ([^ \(\)]*)\) \(\[?(${IP_ADDRESS})\]?\)( \(envelope-sender <\S+>\))? by (\S+)/) {
$rdns = $1; $helo = $2; $ip = $3; $by = $5;
}
elsif (/^(\S+) \((\S*)\@\[?(${IP_ADDRESS})\]?\)( \(envelope-sender <\S+>\))? by (\S+)/) {
# note: absence of HELO means that it matched rDNS in qmail-land
$helo = $rdns = $1; $ident = $2; $ip = $3; $by = $5;
}
elsif (/^(\S+) \(\[?(${IP_ADDRESS})\]?\)( \(envelope-sender <\S+>\))? by (\S+)/) {
$helo = $rdns = $1; $ip = $2; $by = $4;
}
# qmail doesn't perform rDNS requests by itself, but is usually called
# by tcpserver or a similar daemon that passes rDNS information to qmail-smtpd.
# If qmail puts something else than "unknown" in the rDNS field, it means that
# it received this information from the daemon that called it. If qmail-smtpd
# writes "Received: from unknown", it means that either the remote has no
# rDNS, or qmail was called by a daemon that didn't gave the rDNS information.
if ($rdns ne "unknown") {
$mta_looked_up_dns = 1;
} else {
$rdns = '';
}
goto enough;
}
# /MiB
# Received: from [193.220.176.134] by web40310.mail.yahoo.com via HTTP;
# Wed, 12 Feb 2003 14:22:21 PST
if (/ via HTTP$/ && /^\[(${IP_ADDRESS})\] by (\S+) via HTTP$/) {
$ip = $1; $by = $2; goto enough;
}
# Received: from 192.168.5.158 ( [192.168.5.158]) as user jason@localhost by mail.reusch.net with HTTP; Mon, 8 Jul 2002 23:24:56 -0400
if (/^(\S+) \( \[(${IP_ADDRESS})\]\).*? by (\S+) /) {
# TODO: is $1 helo?
$ip = $2; $by = $3; goto enough;
}
# Received: from (64.52.135.194 [64.52.135.194]) by mail.unearthed.com with ESMTP id BQB0hUH2 Thu, 20 Feb 2003 16:13:20 -0700 (PST)
if (/^\((\S+) \[(${IP_ADDRESS})\]\) by (\S+) /) {
$helo = $1; $ip = $2; $by = $3; goto enough;
}
# Received: from [65.167.180.251] by relent.cedata.com (MessageWall 1.1.0) with SMTP; 20 Feb 2003 23:57:15 -0000
if (/^\[(${IP_ADDRESS})\] by (\S+) /) {
$ip = $1; $by = $2; goto enough;
}
# from ([172.16.1.78]) by email2.codeworksonline.com with Microsoft SMTPSVC(5.0.2195.6713); Wed, 6 Sep 2006 21:14:29 -0400
# from (130.215.36.186) by mcafee.wpi.edu via smtp id 021b_7e19a55a_ea7e_11da_83a9_00304811e63a; Tue, 23 May 2006 13:06:35 -0400
# from ([172.21.2.10]) by out-relay4.mtahq.org with ESMTP id 4420961.8281; Tue, 22 Aug 2006 17:53:08 -0400
if (/^\(\[?(${IP_ADDRESS})\]?\) by (\S+) /) {
$ip = $1; $by = $2; goto enough;
}
# Received: from acecomms [202.83.84.95] by mailscan.acenet.net.au [202.83.84.27] with SMTP (MDaemon.PRO.v5.0.6.R) for <spamassassin-talk@lists.sourceforge.net>; Fri, 21 Feb 2003 09:32:27 +1000
if (/^(\S+) \[(${IP_ADDRESS})\] by (\S+) \[${IP_ADDRESS}\] with /) {
$mta_looked_up_dns = 1;
$helo = $1; $ip = $2; $by = $3;
goto enough;
}
# Received: smtp510.aspkunden.de [(134.97.4.21)] by mail.aspemail.de (134.97.4.24) (MDaemon PRO v19.0.2) with ESMTP id md50018233933.msg; Tue, 16 Jul 2019 11:39:22 +0200
if (/^(\S+) \[\((${IP_ADDRESS})\)\] by (\S+) \(${IP_ADDRESS}\) /) {
$helo = $1; $ip = $2; $by = $3;
goto enough;
}
# Received: from mail.sxptt.zj.cn ([218.0.185.24]) by dogma.slashnull.org
# (8.11.6/8.11.6) with ESMTP id h2FH0Zx11330 for <webmaster@efi.ie>;
# Sat, 15 Mar 2003 17:00:41 GMT
if (/^(\S+) \(\[(${IP_ADDRESS})\]\) by (\S+) \(/) { # sendmail
$mta_looked_up_dns = 1;
$helo = $1; $ip = $2; $by = $3; goto enough;
}
# Received: from umr-mail7.umr.edu (umr-mail7.umr.edu [131.151.1.64]) via ESMTP by mrelay1.cc.umr.edu (8.12.1/) id h06GHYLZ022481; Mon, 6 Jan 2003 10:17:34 -0600
# Received: from Agni (localhost [::ffff:127.0.0.1]) (TLS: TLSv1/SSLv3, 168bits,DES-CBC3-SHA) by agni.forevermore.net with esmtp; Mon, 28 Oct 2002 14:48:52 -0800
# Received: from gandalf ([4.37.75.131]) (authenticated bits=0) by herald.cc.purdue.edu (8.12.5/8.12.5/herald) with ESMTP id g9JLefrm028228 for <spamassassin-talk@lists.sourceforge.net>; Sat, 19 Oct 2002 16:40:41 -0500 (EST)
# Received: from bushinternet.com (softdnserr [::ffff:61.99.99.67]) by mail.cs.helsinki.fi with esmtp; Fri, 22 Aug 2003 12:25:41 +0300
if (/^(\S+) \((\S+) \[(${IP_ADDRESS})\]\).*? by (\S+)\b/) { # sendmail
if ($2 eq 'softdnserr') {
$mta_looked_up_dns = 0; # bug 2326: couriertcpd
} else {
$mta_looked_up_dns = 1; $rdns = $2;
}
$helo = $1; $ip = $3; $by = $4; goto enough;
}
# from jsoliday.acs.internap.com ([63.251.66.24.63559]) by
# mailhost.acs.internap.com with esmtp (v3.35.1) id 1GNrLz-000295-00;
# Thu, 14 Sep 2006 09:34:07 -0400
if (/^(\S+) \(\[(${IP_ADDRESS})(?:[.:]\d+)?\]\).*? by (\S+) /) {
$mta_looked_up_dns = 1;
$helo = $1; $ip = $2; $by = $3; goto enough;
}
# Received: from roissy (p573.as1.exs.dublin.eircom.net [159.134.226.61])
# (authenticated bits=0) by slate.dublin.wbtsystems.com (8.12.6/8.12.6)
# with ESMTP id g9MFWcvb068860 for <jm@jmason.org>;
# Tue, 22 Oct 2002 16:32:39 +0100 (IST)
if (/^(\S+) \((\S+) \[(${IP_ADDRESS})\]\)(?: \(authenticated bits=\d+\))? by (\S+) \(/) { # sendmail
$mta_looked_up_dns = 1;
$helo = $1; $rdns = $2; $ip = $3; $by = $4; goto enough;
}
# Identify fetch-from-server incidents:
# Fetchmail:
# Received: from cabbage.jmason.org [127.0.0.1]
# by localhost with IMAP (fetchmail-5.9.0)
# for jm@localhost (single-drop); Thu, 13 Mar 2003 20:39:56 -0800 (PST)
#
# Getmail:
# Received: from pop3.mail.dk (195.41.46.251) by loki.valhalla with POP3;
# 14 Apr 2010 11:14:29 -0000
#
if (/with (?:POP3|IMAP)/) {
$self->found_pop_fetcher_sig();
return 0; # skip mail fetcher handovers
}
# Let's try to support a few qmailish formats in one;
# http://issues.apache.org/SpamAssassin/show_bug.cgi?id=2744#c14 :
# Received: from unknown (HELO feux01a-isp) (213.199.4.210) by totor.bouissou.net with SMTP; 1 Nov 2003 07:05:19 -0000
# Received: from adsl-207-213-27-129.dsl.lsan03.pacbell.net (HELO merlin.net.au) (Owner50@207.213.27.129) by totor.bouissou.net with SMTP; 10 Nov 2003 06:30:34 -0000
if (/^(\S+) \((?:HELO|EHLO) ([^\)]*)\) \((\S*@)?\[?(${IP_ADDRESS})\]?\).* by (\S+) /)
{
$mta_looked_up_dns = 1;
$rdns = $1;
$helo = $2;
$ident = (defined $3) ? $3 : '';
$ip = $4;
$by = $5;
if ($ident) {
$ident =~ s/\@$//;
}
goto enough;
}
# Received: from x1-6-00-04-bd-d2-e0-a3.k317.webspeed.dk (benelli@80.167.158.170) by totor.bouissou.net with SMTP; 5 Nov 2003 23:18:42 -0000
if (/^(\S+) \((\S*@)?\[?(${IP_ADDRESS})\]?\).* by (\S+) /)
{
$mta_looked_up_dns = 1;
# bug 2744 notes that if HELO == rDNS, qmail drops it.
$rdns = $1; $helo = $rdns; $ident = (defined $2) ? $2 : '';
$ip = $3; $by = $4;
if ($ident) { $ident =~ s/\@$//; }
goto enough;
}
# Received: from [129.24.215.125] by ws1-7.us4.outblaze.com with http for
# _bushisevil_@mail.com; Thu, 13 Feb 2003 15:59:28 -0500
if (/ with http for / && /^\[(${IP_ADDRESS})\] by (\S+) with http for /) {
$ip = $1; $by = $2; goto enough;
}
# Received: from snake.corp.yahoo.com(216.145.52.229) by x.x.org via smap (V1.3)
# id xma093673; Wed, 26 Mar 03 20:43:24 -0600
if (/ via smap / && /^(\S+)\((${IP_ADDRESS})\) by (\S+) via smap /) {
$mta_looked_up_dns = 1;
$rdns = $1; $ip = $2; $by = $3; goto enough;
}
# Received: from smtp.greyware.com(208.14.208.51, HELO smtp.sff.net) by x.x.org via smap (V1.3)
# id xma002908; Fri, 27 Feb 04 14:16:56 -0800
if (/^(\S+)\((${IP_ADDRESS}), (?:HELO|EHLO) (\S*)\) by (\S+) via smap /) {
$mta_looked_up_dns = 1;
$rdns = $1; $ip = $2; $helo = $3; $by = $4; goto enough;
}
# Received: from [192.168.0.71] by web01-nyc.clicvu.com (Post.Office MTA
# v3.5.3 release 223 ID# 0-64039U1000L100S0V35) with SMTP id com for
# <x@x.org>; Tue, 25 Mar 2003 11:42:04 -0500
if (/ \(Post/ && /^\[(${IP_ADDRESS})\] by (\S+) \(Post/) {
$ip = $1; $by = $2; goto enough;
}
# Received: from [127.0.0.1] by euphoria (ArGoSoft Mail Server
# Freeware, Version 1.8 (1.8.2.5)); Sat, 8 Feb 2003 09:45:32 +0200
if (/ \(ArGoSoft/ && /^\[(${IP_ADDRESS})\] by (\S+) \(ArGoSoft/) {
$ip = $1; $by = $2; goto enough;
}
# Received: from 157.54.8.23 by inet-vrs-05.redmond.corp.microsoft.com
# (InterScan E-Mail VirusWall NT); Thu, 06 Mar 2003 12:02:35 -0800
# Received: from 10.165.130.62 by CNNIMAIL12.CNN.COM (SMTPL release 1.0d) with TCP; Fri, 1 Sep 2006 20:28:14 -0400
if (/^(${IP_ADDRESS}) by (\S+) \((?:SMTPL|InterScan)\b/) {
$ip = $1; $by = $2; goto enough;
}
# Received: from faerber.muc.de by slarti.muc.de with BSMTP (rsmtp-qm-ot 0.4)
# for asrg@ietf.org; 7 Mar 2003 21:10:38 -0000
if (/ with BSMTP/ && /^\S+ by \S+ with BSMTP/) {
return 0; # BSMTP != a TCP/IP handover, ignore it
}
# Received: from spike (spike.ig.co.uk [193.32.60.32]) by mail.ig.co.uk with
# SMTP id h27CrCD03362 for <asrg@ietf.org>; Fri, 7 Mar 2003 12:53:12 GMT
if (/^(\S+) \((\S+) \[(${IP_ADDRESS})\]\) by (\S+) with /) {
$mta_looked_up_dns = 1;
$helo = $1; $rdns = $2; $ip = $3; $by = $4; goto enough;
}
# Received: from customer254-217.iplannetworks.net (HELO AGAMENON)
# (baldusi@200.69.254.217 with plain) by smtp.mail.vip.sc5.yahoo.com with
# SMTP; 11 Mar 2003 21:03:28 -0000
if (/^(\S+) \((?:HELO|EHLO) (\S*)\) \((?:(\S+)\@)?(${IP_ADDRESS}).*?\) by (\S+) with /) {
$mta_looked_up_dns = 1;
$rdns = $1; $helo = $2; $ip = $4; $by = $5;
$ident = $3 if defined $3;
goto enough;
}
# Received: from [192.168.1.104] (account nazgul HELO [192.168.1.104])
# by somewhere.com (CommuniGate Pro SMTP 3.5.7) with ESMTP-TLS id 2088434;
# Fri, 07 Mar 2003 13:05:06 -0500
if (/^\[(${IP_ADDRESS})\] \((?:account \S+ )?(?:HELO|EHLO) (\S*)\) by (\S+) \(/) {
$ip = $1; $helo = $2; $by = $3; goto enough;
}
# Received: from host.example.com ([192.0.2.1] verified)
# by mail.example.net (CommuniGate Pro SMTP 5.1.13)
# with ESMTP id 9786656 for user@example.net; Thu, 27 Mar 2008 15:08:17 +0600
if (/ \(CommuniGate Pro/ && /^(\S+) \(\[(${IP_ADDRESS})\] verified\) by (\S+) \(/) {
$mta_looked_up_dns = 1;
$rdns = $1; $helo = $1; $ip = $2; $by = $3; goto enough;
}
# Received: from ([10.0.0.6]) by mail0.ciphertrust.com with ESMTP ; Thu,
# 13 Mar 2003 06:26:21 -0500 (EST)
if (/^\(\[(${IP_ADDRESS})\]\) by (\S+) with /) {
$ip = $1; $by = $2; goto enough;
}
# Received: from ironport.com (10.1.1.5) by a50.ironport.com with ESMTP; 01 Apr 2003 12:00:51 -0800
# Received: from dyn-81-166-39-132.ppp.tiscali.fr (81.166.39.132) by cpmail.dk.tiscali.com (6.7.018)
if (/^([^\d]\S+) \((${IP_ADDRESS})\) by (\S+) /) {
$helo = $1; $ip = $2; $by = $3; goto enough;
}
# Received: from scv3.apple.com (scv3.apple.com) by mailgate2.apple.com (Content Technologies SMTPRS 4.2.1) with ESMTP id <T61095998e1118164e13f8@mailgate2.apple.com>; Mon, 17 Mar 2003 17:04:54 -0800
# bug 4704: Only let this match Content Technologies so it stops breaking things that come after it by matching first
if (/^\S+ \(\S+\) by \S+ \(Content Technologies /) {
return 0; # useless without the $ip anyway!
}
# Received: from 01al10015010057.ad.bls.com ([90.152.5.141] [90.152.5.141])
# by aismtp3g.bls.com with ESMTP; Mon, 10 Mar 2003 11:10:41 -0500
if (/^(\S+) \(\[(${IP_ADDRESS})\] \[(\S+)\]\) by (\S+) with /) {
# not sure what $3 is ;)
$helo = $1; $ip = $2; $by = $4;
goto enough;
}
# Received: from 206.47.0.153 by dm3cn8.bell.ca with ESMTP (Tumbleweed MMS
# SMTP Relay (MMS v5.0)); Mon, 24 Mar 2003 19:49:48 -0500
if (/^(${IP_ADDRESS}) by (\S+) with /) {
$ip = $1; $by = $2;
goto enough;
}
# Received: from pobox.com (h005018086b3b.ne.client2.attbi.com[66.31.45.164])
# by rwcrmhc53.attbi.com (rwcrmhc53) with SMTP id <2003031302165605300suph7e>;
# Thu, 13 Mar 2003 02:16:56 +0000
if (/^(\S+) \((\S+)\[(${IP_ADDRESS})\]\) by (\S+) /) {
$mta_looked_up_dns = 1;
$helo = $1; $rdns = $2; $ip = $3; $by = $4; goto enough;
}
# Received: from [10.128.128.81]:50999 (HELO dfintra.f-secure.com) by fsav4im2 ([10.128.128.74]:25) (F-Secure Anti-Virus for Internet Mail 6.0.34 Release) with SMTP; Tue, 5 Mar 2002 14:11:53 -0000
if (/^\[(${IP_ADDRESS})\]\S+ \((?:HELO|EHLO) (\S*)\) by (\S+) /) {
$ip = $1; $helo = $2; $by = $3; goto enough;
}
# Received: from 62.180.7.250 (HELO daisy) by smtp.altavista.de (209.228.22.152) with SMTP; 19 Sep 2002 17:03:17 +0000
if (/^(${IP_ADDRESS}) \((?:HELO|EHLO) (\S*)\) by (\S+) /) {
$ip = $1; $helo = $2; $by = $3; goto enough;
}
# Received: from oemcomputer [63.232.189.195] by highstream.net (SMTPD32-7.07) id A4CE7F2A0028; Sat, 01 Feb 2003 21:39:10 -0500
if (/^(\S+) \[(${IP_ADDRESS})\] by (\S+) /) {
$helo = $1; $ip = $2; $by = $3; goto enough;
}
# from nodnsquery(192.100.64.12) by herbivore.monmouth.edu via csmap (V4.1) id srcAAAyHaywy
if (/^(\S+)\((${IP_ADDRESS})\) by (\S+) /) {
$rdns = $1; $ip = $2; $by = $3; goto enough;
}
# Received: from [192.168.0.13] by <server> (MailGate 3.5.172) with SMTP;
# Tue, 1 Apr 2003 15:04:55 +0100
if (/^\[(${IP_ADDRESS})\] by (\S+) \(MailGate /) {
$ip = $1; $by = $2; goto enough;
}
# Received: from jmason.org (unverified [195.218.107.131]) by ni-mail1.dna.utvinternet.net <B0014212518@ni-mail1.dna.utvinternet.net>; Tue, 11 Feb 2003 12:18:12 +0000
if (/^(\S+) \(unverified \[(${IP_ADDRESS})\]\) by (\S+) /) {
$helo = $1; $ip = $2; $by = $3; goto enough;
}
# # from 165.228.131.11 (proxying for 139.130.20.189) (SquirrelMail authenticated user jmmail) by jmason.org with HTTP
# if (/^from (\S+) \(proxying for (${IP_ADDRESS})\) \([A-Za-z][^\)]+\) by (\S+) with /) {
# $ip = $2; $by = $3; goto enough;
# }
if (/^(${IP_ADDRESS}) \([A-Za-z][^\)]+\) by (\S+) with /) {
$ip = $1; $by = $2; goto enough;
}
# Received: from [212.87.144.30] (account seiz [212.87.144.30] verified) by x.imd.net (CommuniGate Pro SMTP 4.0.3) with ESMTP-TLS id 5026665 for spamassassin-talk@lists.sourceforge.net; Wed, 15 Jan 2003 16:27:05 +0100
# bug 4704 This pattern was checked as just an Exim format, but it does exist elsewhere
# Received: from [206.51.230.145] (helo=t-online.de)
# by mxeu2.kundenserver.de with ESMTP (Nemesis),
# id 0MKpdM-1CkRpr14PF-000608; Fri, 31 Dec 2004 19:49:15 +0100
# Received: from [218.19.142.229] (helo=hotmail.com ident=yiuhyotp)
# by yzordderrex with smtp (Exim 3.35 #1 (Debian)) id 194BE5-0005Zh-00; Sat, 12 Apr 2003 03:58:53 +0100
if (/^\[(${IP_ADDRESS})\] \(([^\)]+)\) by (\S+) /) {
$ip = $1; my $sub = $2; $by = $3;
$sub =~ s/helo=(\S+)// and $helo = $1;
$sub =~ s/ident=(\S*)// and $ident = $1;
goto enough;
}
# Received: from mtsbp606.email-info.net (?dXqpg3b0hiH9faI2OxLT94P/YKDD3rQ1?@64.253.199.166) by kde.informatik.uni-kl.de with SMTP; 30 Apr 2003 15:06:29
if (/^(\S+) \((?:\S+\@)?(${IP_ADDRESS})\) by (\S+) with /) {
$rdns = $1; $ip = $2; $by = $3; goto enough;
}
# Obtuse smtpd: http://www.obtuse.com/
# Received: from TCE-E-7-182-54.bta.net.cn(202.106.182.54) via SMTP
# by st.tahina.priv.at, id smtpdEDUB8h; Sun Nov 13 14:50:12 2005
# Received: from pl027.nas934.d-osaka.nttpc.ne.jp(61.197.82.27), claiming to be "foo.woas.net" via SMTP
# by st.tahina.priv.at, id smtpd1PBsZT; Sun Nov 13 15:38:52 2005
if (/^(\S+)\((${IP_ADDRESS})\)(?:, claiming to be "(\S+)")? via \S+ by (\S+),/) {
$rdns = $1; $ip = $2; $helo = (defined $3) ? $3 : ''; $by = $4;
if ($1 ne 'UNKNOWN') {
$mta_looked_up_dns = 1;
$rdns = $1;
}
goto enough;
}
# Yahoo Authenticated SMTP; Bug #6535
# from itrqtnlnq (lucilleskinner@93.124.107.183 with login) by smtp111.mail.ne1.yahoo.com with SMTP; 17 Jan 2011 08:23:27 -0800 PST
if (/^(\S+) \((\S+)@(${IP_ADDRESS}) with login\) by (\S+\.yahoo\.com) with SMTP/) {
$helo = $1; $ip = $3; $by = $4; goto enough;
}
# a synthetic header, generated internally:
# Received: X-Originating-IP: 1.2.3.4
if (/^X-Originating-IP: (${IP_ADDRESS})$/) {
$ip = $1; $by = ''; goto enough;
}
## STUFF TO IGNORE ##
# Received: from raptor.research.att.com (bala@localhost) by
# raptor.research.att.com (SGI-8.9.3/8.8.7) with ESMTP id KAA14788
# for <asrg@example.com>; Fri, 7 Mar 2003 10:37:56 -0500 (EST)
# make this localhost-specific, so we know it's safe to ignore
if (/^\S+ \([^\s\@]+\@${LOCALHOST}\) by \S+ \(/) { return 0; }
# from paul (helo=felix) by felix.peema.org with local-esmtp (Exim 4.43)
# id 1Ccq0j-0002k2-Lk; Fri, 10 Dec 2004 19:01:01 +0000
# Exim doco says this is local submission, cf switch -oMr
if (/^\S+ \S+ by \S+ with local-e?smtp /) { return 0; }
# from 127.0.0.1 (AVG SMTP 7.0.299 [265.6.8]); Wed, 05 Jan 2005 15:06:48 -0800
if (/^127\.0\.0\.1 \(AVG SMTP \S+ \[\S+\]\)/) { return 0; }
# from qmail-scanner-general-admin@lists.sourceforge.net by alpha by uid 7791 with qmail-scanner-1.14 (spamassassin: 2.41. Clear:SA:0(-4.1/5.0):. Processed in 0.209512 secs)
if (/^\S+\@\S+ by \S+ by uid \S+ /) { return 0; }
# Received: from DSmith1204@aol.com by imo-m09.mx.aol.com (mail_out_v34.13.) id 7.53.208064a0 (4394); Sat, 11 Jan 2003 23:24:31 -0500 (EST)
if (/^\S+\@\S+ by \S+ /) { return 0; }
# Received: from Unknown/Local ([?.?.?.?]) by mailcity.com; Fri, 17 Jan 2003 15:23:29 -0000
if (/^Unknown\/Local \(/) { return 0; }
# Received: from localhost (mailnull@localhost) by x.org (8.12.6/8.9.3)
# with SMTP id h2R2iivG093740; Wed, 26 Mar 2003 20:44:44 -0600
# (CST) (envelope-from x@x.org)
# Received: from localhost (localhost [127.0.0.1]) (uid 500) by mail with local; Tue, 07 Jan 2003 11:40:47 -0600
if (/^${LOCALHOST} \((?:\S+\@)?${LOCALHOST}[\)\[]/) { return 0; }
# Received: from olgisoft.com (127.0.0.1) by 127.0.0.1 (EzMTS MTSSmtp
# 1.55d5) ; Thu, 20 Mar 03 10:06:43 +0100 for <asrg@ietf.org>
if (/^\S+ \((?:\S+\@)?${LOCALHOST}\) /) { return 0; }
# Received: from casper.ghostscript.com (raph@casper [127.0.0.1]) h148aux8016336verify=FAIL); Tue, 4 Feb 2003 00:36:56 -0800
if (/^\S+ \(\S+\@\S+ \[${LOCALHOST}\]\) /) { return 0; }
# Received: from (AUTH: e40a9cea) by vqx.net with esmtp (courier-0.40) for <asrg@ietf.org>; Mon, 03 Mar 2003 14:49:28 +0000
if (/^\(AUTH: \S+\) by \S+ with /) { return 0; }
# from localhost (localhost [[UNIX: localhost]]) by home.barryodonovan.com
# (8.12.11/8.12.11/Submit) id iBADHRP6011034; Fri, 10 Dec 2004 13:17:27 GMT
if (/^localhost \(localhost \[\[UNIX: localhost\]\]\) by /) { return 0; }
# Internal Amazon traffic
# Received: from dc-mail-3102.iad3.amazon.com by mail-store-2001.amazon.com with ESMTP (peer crosscheck: dc-mail-3102.iad3.amazon.com)
if (/^\S+\.amazon\.com by \S+\.amazon\.com with ESMTP \(peer crosscheck: /) { return 0; }
# Received: from GWGC6-MTA by gc6.jefferson.co.us with Novell_GroupWise; Tue, 30 Nov 2004 10:09:15 -0700
if (/^[^\.]+ by \S+ with Novell_GroupWise/) { return 0; }
# Received: from no.name.available by [165.224.43.143] via smtpd (for [165.224.216.89]) with ESMTP; Fri, 28 Jan 2005 13:06:39 -0500
# Received: from no.name.available by [165.224.216.88] via smtpd (for lists.sourceforge.net [66.35.250.206]) with ESMTP; Fri, 28 Jan 2005 15:42:30 -0500
# These are from an internal host protected by a Raptor firewall, to hosts
# outside the firewall. We can only ignore the handover since we don't have
# enough info in those headers; however, from googling, it appears that
# all samples are cases where the handover is safely ignored.
if (/^no\.name\.available by \S+ via smtpd \(for /) { return 0; }
# from 156.56.111.196 by blazing.arsecandle.org (envelope-from <gentoo-announce-return-530-rod=arsecandle.org@lists.gentoo.org>, uid 502) with qmail-scanner-1.24 (clamdscan: 0.80/594. f-prot: 4.4.2/3.14.11. Clear:RC:0(156.56.111.196):. Processed in 0.288806 secs); 06 Feb 2005 21:11:38 -0000
# these are safe to ignore. the previous handover line has the full
# details of the handover described here, it's just qmail-scanner
# logging a little more.
if (/^\S+ by \S+ \(.{0,100}\) with qmail-scanner/) {
if (defined $envfrom) {
$envfrom =~ s/^\s*<*//gs;
$envfrom =~ s/>*\s*$//gs;
$envfrom =~ s/[\s\000\#\[\]\(\)\<\>\|]/!/gs;
}
$self->{qmail_scanner_env_from} = $envfrom; # hack!
return 0;
}
# Received: from mmail by argon.connect.org.uk with local (connectmail/exim)
# id 18tOsg-0008FX-00; Thu, 13 Mar 2003 09:20:06 +0000
if (/^\S+ by \S+ with local/) { return 0; }
# Local unix socket handover from Cyrus, tested with v2.3.14
# Received: from testintranator.net.vm ([unix socket])_ by testintranator.net.vm (Cyrus v2.3.14) with LMTPA;_ Tue, 21 Jul 2009 14:34:14 +0200
# Attention: Actually the received header is parsed as "testintranator.net.vm ([unix socket]) by testintranator.net.vm (Cyrus v2.3.14) with LMTPA", "from" is omitted.
if (/^\S+ \(\[unix socket\]\) by \S+ \(Cyrus v[0-9]*?\.[0-9]*?\.[0-9]*?\) with LMTPA/) { return 0; }
# HANDOVERS WE KNOW WE CAN'T DEAL WITH: TCP transmission, but to MTAs that
# just don't log enough info for us to use (ie. no IP address present).
# Note: "return 0" is strongly recommended here, unless you're sure
# the regexp won't match something in the field; otherwise ALL_TRUSTED may
# fire even in the presence of an unparseable Received header.
# Received: from CATHY.IJS.SI by CATHY.IJS.SI (PMDF V4.3-10 #8779) id <01KTSSR50NSW001MXN@CATHY.IJS.SI>; Fri, 21 Mar 2003 20:50:56 +0100
# Received: from MATT_LINUX by hippo.star.co.uk via smtpd (for mail.webnote.net [193.120.211.219]) with SMTP; 3 Jul 2002 15:43:50 UT
# Received: from cp-its-ieg01.mail.saic.com by cpmx.mail.saic.com for me@jmason.org; Tue, 23 Jul 2002 14:09:10 -0700
if (/^\S+ by \S+ (?:with|via|for|\()/) { return 0; }
# from senmail2.senate.gov with LMTP by senmail2 (3.0.2/sieved-3-0-build-942) for <example@vandinter.org>; Fri, 30 Jun 2006 10:58:41 -0400
# from zimbramail.artsit.org.uk (unverified) by MAILSWEEP.birminghamartsit.org.uk (Clearswift SMTPRS 5.1.7) with ESMTP id <T78926b35f2c0a80003da8@MAILSWEEP.birminghamartsit.org.uk> for <discuss@lists.surbl.org>; Tue, 30 May 2006 15:56:15 +0100
if (/^\S+ (?:(?:with|via|for) \S+|\(unverified\)) by\b/) { return 0; }
# from MjA3NDc4Mg (unknown) by ismtpd0001p1lon1.sendgrid.net (SG) with HTTP id aqHKNX2kSp-HiqspAa-uvw for <email@e.example.com>; Thu, 02 Apr 2020 07:53:55.516 +0000 (UTC)
if (/^\S+ \(unknown\) by \S+ \(SG\) with \b/) { return 0; }
# from localhost (example.com [local]) by example.com (OpenSMTPD) with ESMTPA id 5db34e0d for <email@example.com>; Tue, 7 Apr 2020 01:38:29 -0600 (MDT)
if (/^\S+ \(\S+ \[local\]\) by \S+ \(OpenSMTPD\) with \b/) { return 0; }
# from DL1GSPMX02 (dl1gspmx02.gamestop.com) by email.ebgames.com (LSMTP for Windows NT v1.1b) with SMTP id <21.000575A0@email.ebgames.com>; Tue, 12 Sep 2006 21:06:43 -0500
if (/\(LSMTP for/) { return 0; }
# from ([127.0.0.1]) with MailEnable ESMTP; Wed, 10 Jul 2019 10:29:59 +0300
if (/^\(\[${LOCALHOST}\]\) with MailEnable /) { return 0; }
# from facebook.com (RrlQsUbrndsQ6/zbJaSzSPcmy3GwqE5h6IukkE5GGBIJgonAFnoQE3L+9tv2TU3e 2401:db00:1110:50e8:face:0000:002f:0000)
# by facebook.com with Thrift id 423753524b5011e9a83e248a0796a3b2-169bd530; Wed, 20 Mar 2019 13:39:29 -0700
if (/^facebook\.com \([^\)]+\) by facebook\.com with Thrift id \S+$/) { return 0; }
# from 384836569573 named unknown by gmailapi.google.com with HTTPREST; Wed, 6 Mar 2019 03:39:24 -0500
if (/^\S+ named \S+ by gmailapi\.google\.com with HTTPREST$/) { return 0; }
# from mail.payex.com id <B5b8f11e30004>; Wed, 05 Sep 2018 01:14:43 +0200
if (/^\S+ id \S+$/) { return 0; }
# from [<4124973-137966-3089@be2.maropost.com>] ([<4124973-137966-3089@be2.maropost.com>] helo=maropost.com) by 643852-mailer2 (envelope-from 4124973-137966-3089@be2.maropost.com)
# (Jetsend MTA 0.0.1 with ESMTP; Fri Sep 14 14:36:56 EDT 2018
if (/^\[<.*? \(Jetsend/) { return 0; }
# if at this point we still haven't figured out the HELO string, see if we
# can't just guess
if (!$helo && /^(\S+)[^-A-Za-z0-9\.]/) { $helo = $1; }
}
# ---------------------------------------------------------------------------
elsif (s/^FROM //) {
# simta: http://rsug.itd.umich.edu/software/simta/
# Note the ugly uppercase FROM/BY/ID
# Received: FROM hackers.mr.itd.umich.edu (smtp.mail.umich.edu [141.211.14.81])
# BY madman.mr.itd.umich.edu ID 434B508E.174A6.13932 ; 11 Oct 2005 01:41:34 -0400
# Received: FROM [192.168.1.24] (s233-64-90-216.try.wideopenwest.com [64.233.216.90])
# BY hackers.mr.itd.umich.edu ID 434B5051.8CDE5.15436 ; 11 Oct 2005 01:40:33 -0400
# Received: FROM helo (1.2.3.4 [1.2.3.4]) BY xxx.com (Rockliffe SMTPRA 10.3.0)
# WITH SMTP ID <B0065361981@xxx.com> FOR <foo@bar.net>; Tue, 6 Nov 2018 07:41:26 +0200
if (/^(\S+) \((\S+) \[(${IP_ADDRESS})\]\) BY (\S+) (?:\([^\)]+\) WITH SMTP )?ID <?(\S+?)>?(?: FOR <[^>]+>)?$/ ) {
$mta_looked_up_dns = 1;
$helo = $1; $rdns = $2; $ip = $3; $by = $4; $id = $5;
$rdns = '' if $rdns eq 'unverified';
goto enough;
}
}
# ---------------------------------------------------------------------------
elsif (s/^\(from //) {
# Norton AntiVirus Gateway
# Received: (from localhost [24.180.47.240])
# by host.name (NAVGW 2.5.2.12) with SMTP id M2006060503484615455
# for <user@domain.co.uk>; Mon, 05 Jun 2006 03:48:47 +0100
if (/^(\S*) \[(${IP_ADDRESS})\]\) by (\S+) \(NAVGW .*?\) with /) {
$helo = $1; $ip = $2; $by = $3;
goto enough;
}
# header produced by command line /usr/bin/sendmail -t -f username@example.com
# Received: (from username@localhost) by home.example.com
# (8.12.11/8.12.11/Submit) id iBADHRP6011034; Fri, 10 Dec 2004 13:17:27 GMT
if (/^\S+\@localhost\) by \S+ /) { return 0; }
# Received: (from vashugins@juno.com) by m06.lax.untd.com (jqueuemail) id LRVB3JAJ; Fri, 02 Jun 2006 08:15:21 PDT
if (/^[^\s\@]+\@[^)]+\) by \S+\(jqueuemail\) id [^\s;]+/) { return 0; }
}
# ---------------------------------------------------------------------------
# FALL-THROUGH: OK, at this point let's try some general patterns for things
# we may not have already parsed out.
if (!$ip && /\[(${IP_ADDRESS})\]/) { $ip = $1; }
# ---------------------------------------------------------------------------
# We need to have a minimal amount of information to have a useful parse.
# If we have the IP and the "by" name, move forward. If we don't, we'll
# drop into the unparseable area.
if ($ip && $by) { goto enough; }
# Ok, we can't handle this header, go ahead and return that.
return;
# ---------------------------------------------------------------------------
enough:
# OK, line parsed (at least partially); now deal with the contents
# flag handovers we couldn't get an IP address from at all
if ($ip eq '') {
dbg("received-header: could not parse IP address from: $_");
}
# DISABLED: if we cut out localhost-to-localhost SMTP handovers,
# we will give FPs on SPF checks -- since the SMTP "MAIL FROM" addr
# will be recorded, but we won't have the relays handover recorded
# for that SMTP transaction, so we wind up checking the wrong IP
# for the addr.
if (0) {
if ($ip eq '127.0.0.1') {
dbg("received-header: ignoring localhost handover");
return 0; # ignore localhost handovers
}
}
# Strip ending dot, Bug 7810
$rdns =~ s/\.+\z//;
if ($rdns =~ /^unknown$/i || $rdns =~ /^\[/) {
$rdns = ''; # some MTAs seem to do this
}
$ip =~ s/^ipv6://i; # remove "IPv6:" prefix
$ip =~ s/^\[//; $ip =~ s/\]\z//;
# IPv6 Scoped Address (RFC 4007, RFC 6874, RFC 3986 "unreserved" charset)
$ip =~ s/%[A-Z0-9._~-]*\z//si; # scoped address? remove <zone_id>
# remove "::ffff:" prefix from IPv4-mapped-in-IPv6 addresses,
# so we can treat them simply as IPv4 addresses
# (only handles 'alternative form', not 'preferred form' - to be improved)
$ip =~ s/^0*:0*:(?:0*:)*ffff:(\d+\.\d+\.\d+\.\d+)$/$1/i;
$by =~ s/\;$//;
# ensure invalid chars are stripped. Replace with '!' to flag their
# presence, though. NOTE: this means "[1.2.3.4]" IP addr HELO
# strings, which are legit by RFC-2821, look like "!1.2.3.4!".
# still useful though.
my $strip_chars = qr/[\s\000\#\[\]\(\)\<\>\|]/;
$ip =~ s/$strip_chars/!/gs;
$rdns =~ s/$strip_chars/!/gs;
$helo =~ s/$strip_chars/!/gs;
$by =~ s/$strip_chars/!/gs;
$ident =~ s/$strip_chars/!/gs;
if (defined $envfrom) {
$envfrom =~ s/^\s*<*//gs;
$envfrom =~ s/>*\s*$//gs;
$envfrom =~ s/$strip_chars/!/gs;
}
my $relay = {
ip => $ip,
by => $by,
helo => $helo,
id => $id,
ident => $ident,
envfrom => $envfrom,
lc_by => (lc $by),
lc_helo => (lc $helo),
auth => $auth
};
if ($rdns eq '') {
if ($mta_looked_up_dns) {
# we know the MTA always does lookups, so this means the host
# really has no rDNS (rather than that the MTA didn't bother
# looking it up for us).
$relay->{no_reverse_dns} = 1;
$rdns = '';
} else {
$relay->{rdns_not_in_headers} = 1;
}
}
$relay->{rdns} = $rdns;
$relay->{lc_rdns} = lc $rdns;
$self->make_relay_as_string($relay);
my $is_private = ($ip =~ /${IP_PRIVATE}/o);
$relay->{ip_private} = $is_private;
# add it to an internal array so Eval tests can use it
return $relay;
}
sub make_relay_as_string {
my ($self, $relay) = @_;
# as-string rep. use spaces so things like Bayes can tokenize them easily.
# NOTE: when tokenizing or matching, be sure to note that new
# entries may be added to this string later. However, the *order*
# of entries must be preserved, so that regexps that assume that
# e.g. "ip" comes before "helo" will still work.
#
# we could mark envfrom as "undef" if missing? dunno if needed?
my $envfrom = $relay->{envfrom} || '';
my $asstr = "[ ip=$relay->{ip} rdns=$relay->{rdns} helo=$relay->{helo} by=$relay->{by} ident=$relay->{ident} envfrom=$envfrom intl=0 id=$relay->{id} auth=$relay->{auth} msa=0 ]";
dbg("received-header: parsed as $asstr");
$relay->{as_string} = $asstr;
}
# restart the parse if we find a fetchmail marker or similar.
# spamcop does this, and it's a great idea ;)
sub found_pop_fetcher_sig {
my ($self) = @_;
if ($self->{allow_mailfetch_markers}) {
dbg("received-header: found mail fetcher marker, restarting parse");
$self->{relays_trusted} = [ ];
$self->{relays_internal} = [ ];
$self->{relays_external} = [ ];
} else {
dbg("received-header: found mail fetcher marker outside trusted area, ignored");
}
}
# ---------------------------------------------------------------------------
1;
| apache/spamassassin | lib/Mail/SpamAssassin/Message/Metadata/Received.pm | Perl | apache-2.0 | 69,102 |
# 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.
package Lucy::Search::SortSpec;
use Lucy;
our $VERSION = '0.005000';
$VERSION = eval $VERSION;
1;
__END__
| rbevers/lucy | perl/lib/Lucy/Search/SortSpec.pm | Perl | apache-2.0 | 892 |
=head1 SHCrossPowerSpectrum
=over 23
=item SHCrossPowerSpectrum -
Compute the cross-power spectrum of two real functions.
=back
=head1 SYNOPSIS
=over 34
=item SUBROUTINE SHCrossPowerSpectrum (
C1, C2, LMAX, CSPECTRUM )
=back
=over 4
=over 10
=item REAL*8
C1(2, LMAX+1, LMAX+1), C2(2, LMAX+1, LMAX+1), CSPECTRUM(LMAX+1)
=item INTEGER
LMAX
=back
=back
=head1 DESCRIPTION
I<SHCrossPowerSpectrum> will calculate the cross-power spectrum of two functions expressed in real spherical harmonics. For a given degree L, this is explicitly calculated as:
Sum_{i=1}^2 Sum_{m=0}^L C1(i, L+1, m+1) * C2(i, L+1, m+1) .
=head1 ARGUMENTS
=over 10
=item C1
(input) REAL*8, DIMENSION (2, LMAX+1, LMAX+1)
The first function expressed in real spherical harmonics.
=item C2
(input) REAL*8, DIMENSION (2, LMAX+1, LMAX+1)
The second function expressed in real spherical harmonics.
=item LMAX
(input) INTEGER
The maximum spherical harmonic degree for which the cross power spectrum will be calculated.
=item CSPECTRUM
(output) REAL*8, DIMENSION (LMAX+1)
The cross-power spectrum of the two functions.
=back
=head1 SEE ALSO
shpowerl(1), shpowerdensityl(1), shcrosspower(1), shcrosspowerdensityl(1), shpowerspectrum(1), shpowerspectrumdensity(1), shcrosspowerspectrumdensity(1), shadmitcorr(1)
L<http://www.ipgp.jussieu.fr/~wieczor/SHTOOLS/SHTOOLS.html>
=head1 COPYRIGHT AND LICENSE
Copyright 2005-2008 by Mark Wieczorek <wieczor@ipgp.fr>.
This is free software; you can distribute and modify it under the terms of the revised BSD license. | pletnes/SHTOOLS | src/doc/shcrosspowerspectrum.pod | Perl | bsd-3-clause | 1,560 |
# !!!!!!! DO NOT EDIT THIS FILE !!!!!!!
# This file is machine-generated by lib/unicore/mktables from the Unicode
# database, Version 6.2.0. 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';
0000 01F5
01FA 0217
0250 02A8
02B0 02DE
02E0 02E9
0300 0345
0360 0361
0374 0375
037A
037E
0384 038A
038C
038E 03A1
03A3 03CE
03D0 03D6
03DA
03DC
03DE
03E0
03E2 03F3
0401 040C
040E 044F
0451 045C
045E 0486
0490 04C4
04C7 04C8
04CB 04CC
04D0 04EB
04EE 04F5
04F8 04F9
0531 0556
0559 055F
0561 0587
0589
0591 05A1
05A3 05B9
05BB 05C4
05D0 05EA
05F0 05F4
060C
061B
061F
0621 063A
0640 0652
0660 066D
0670 06B7
06BA 06BE
06C0 06CE
06D0 06ED
06F0 06F9
0901 0903
0905 0939
093C 094D
0950 0954
0958 0970
0981 0983
0985 098C
098F 0990
0993 09A8
09AA 09B0
09B2
09B6 09B9
09BC
09BE 09C4
09C7 09C8
09CB 09CD
09D7
09DC 09DD
09DF 09E3
09E6 09FA
0A02
0A05 0A0A
0A0F 0A10
0A13 0A28
0A2A 0A30
0A32 0A33
0A35 0A36
0A38 0A39
0A3C
0A3E 0A42
0A47 0A48
0A4B 0A4D
0A59 0A5C
0A5E
0A66 0A74
0A81 0A83
0A85 0A8B
0A8D
0A8F 0A91
0A93 0AA8
0AAA 0AB0
0AB2 0AB3
0AB5 0AB9
0ABC 0AC5
0AC7 0AC9
0ACB 0ACD
0AD0
0AE0
0AE6 0AEF
0B01 0B03
0B05 0B0C
0B0F 0B10
0B13 0B28
0B2A 0B30
0B32 0B33
0B36 0B39
0B3C 0B43
0B47 0B48
0B4B 0B4D
0B56 0B57
0B5C 0B5D
0B5F 0B61
0B66 0B70
0B82 0B83
0B85 0B8A
0B8E 0B90
0B92 0B95
0B99 0B9A
0B9C
0B9E 0B9F
0BA3 0BA4
0BA8 0BAA
0BAE 0BB5
0BB7 0BB9
0BBE 0BC2
0BC6 0BC8
0BCA 0BCD
0BD7
0BE7 0BF2
0C01 0C03
0C05 0C0C
0C0E 0C10
0C12 0C28
0C2A 0C33
0C35 0C39
0C3E 0C44
0C46 0C48
0C4A 0C4D
0C55 0C56
0C60 0C61
0C66 0C6F
0C82 0C83
0C85 0C8C
0C8E 0C90
0C92 0CA8
0CAA 0CB3
0CB5 0CB9
0CBE 0CC4
0CC6 0CC8
0CCA 0CCD
0CD5 0CD6
0CDE
0CE0 0CE1
0CE6 0CEF
0D02 0D03
0D05 0D0C
0D0E 0D10
0D12 0D28
0D2A 0D39
0D3E 0D43
0D46 0D48
0D4A 0D4D
0D57
0D60 0D61
0D66 0D6F
0E01 0E3A
0E3F 0E5B
0E81 0E82
0E84
0E87 0E88
0E8A
0E8D
0E94 0E97
0E99 0E9F
0EA1 0EA3
0EA5
0EA7
0EAA 0EAB
0EAD 0EB9
0EBB 0EBD
0EC0 0EC4
0EC6
0EC8 0ECD
0ED0 0ED9
0EDC 0EDD
0F00 0F47
0F49 0F69
0F71 0F8B
0F90 0F95
0F97
0F99 0FAD
0FB1 0FB7
0FB9
10A0 10C5
10D0 10F6
10FB
1100 1159
115F 11A2
11A8 11F9
1E00 1E9B
1EA0 1EF9
1F00 1F15
1F18 1F1D
1F20 1F45
1F48 1F4D
1F50 1F57
1F59
1F5B
1F5D
1F5F 1F7D
1F80 1FB4
1FB6 1FC4
1FC6 1FD3
1FD6 1FDB
1FDD 1FEF
1FF2 1FF4
1FF6 1FFE
2000 202E
2030 2046
206A 2070
2074 208E
20A0 20AC
20D0 20E1
2100 2138
2153 2182
2190 21EA
2200 22F1
2300
2302 237A
2400 2424
2440 244A
2460 24EA
2500 2595
25A0 25EF
2600 2613
261A 266F
2701 2704
2706 2709
270C 2727
2729 274B
274D
274F 2752
2756
2758 275E
2761 2767
2776 2794
2798 27AF
27B1 27BE
3000 3037
303F
3041 3094
3099 309E
30A1 30FE
3105 312C
3131 318E
3190 319F
3200 321C
3220 3243
3260 327B
327F 32B0
32C0 32CB
32D0 32FE
3300 3376
337B 33DD
33E0 33FE
4E00 9FA5
AC00 D7A3
D800 FA2D
FB00 FB06
FB13 FB17
FB1E FB36
FB38 FB3C
FB3E
FB40 FB41
FB43 FB44
FB46 FBB1
FBD3 FD3F
FD50 FD8F
FD92 FDC7
FDF0 FDFB
FE20 FE23
FE30 FE44
FE49 FE52
FE54 FE66
FE68 FE6B
FE70 FE72
FE74
FE76 FEFC
FEFF
FF01 FF5E
FF61 FFBE
FFC2 FFC7
FFCA FFCF
FFD2 FFD7
FFDA FFDC
FFE0 FFE6
FFE8 FFEE
FFFC FFFF
1FFFE 1FFFF
2FFFE 2FFFF
3FFFE 3FFFF
4FFFE 4FFFF
5FFFE 5FFFF
6FFFE 6FFFF
7FFFE 7FFFF
8FFFE 8FFFF
9FFFE 9FFFF
AFFFE AFFFF
BFFFE BFFFF
CFFFE CFFFF
DFFFE DFFFF
EFFFE 10FFFF
END
| Bjay1435/capstone | rootfs/usr/share/perl/5.18.2/unicore/lib/In/2_1.pl | Perl | mit | 3,443 |
# !!!!!!! DO NOT EDIT THIS FILE !!!!!!!
# This file is machine-generated by lib/unicore/mktables from the Unicode
# database, Version 8.0.0. 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';
V62
1424
1425
1470
1471
1472
1473
1475
1476
1478
1479
1480
1536
1984
2027
2036
2038
2042
2070
2074
2075
2084
2085
2088
2089
2094
2137
2140
2208
8207
8208
64285
64286
64287
64297
64298
64336
67584
67871
67872
68097
68100
68101
68103
68108
68112
68152
68155
68159
68160
68325
68327
68409
68416
69216
69247
69632
124928
125136
125143
126464
126720
126976
END
| operepo/ope | bin/usr/share/perl5/core_perl/unicore/lib/Bc/R.pl | Perl | mit | 838 |
#-----------------------------------------------------------
# rdpport.pl
# Determine the RDP Port used
#
# History
# 20100713 - created
#
# References
# http://support.microsoft.com/kb/306759
#
# copyright 2010 Quantum Analytics Research, LLC
#-----------------------------------------------------------
package rdpport;
use strict;
my %config = (hive => "System",
hasShortDescr => 1,
hasDescr => 0,
hasRefs => 0,
osmask => 22,
version => 20100713);
sub getConfig{return %config}
sub getShortDescr {
return "Queries System hive for RDP Port";
}
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;
my $key;
::logMsg("Launching rdpport v.".$VERSION);
::rptMsg("rdpport v.".$VERSION); # banner
::rptMsg("(".getHive().") ".getShortDescr()."\n"); # banner
my $reg = Parse::Win32Registry->new($hive);
my $root_key = $reg->get_root_key;
my $ccs = $root_key->get_subkey("Select")->get_value("Current")->get_data();
my $key_path = "ControlSet00".$ccs."\\Control\\Terminal Server\\WinStations\\RDP-Tcp";
if ($key = $root_key->get_subkey($key_path)) {
::rptMsg("rdpport v.".$VERSION);
::rptMsg("");
my $port;
eval {
$port = $key->get_value("PortNumber")->get_data();
::rptMsg("Remote Desktop Listening Port Number = ".$port);
};
::rptMsg("Error getting PortNumber: ".$@) if ($@);
}
else {
::rptMsg($key_path." not found.");
}
}
1 | kefir-/autopsy | RecentActivity/release/rr-full/plugins/rdpport.pl | Perl | apache-2.0 | 1,672 |
#-----------------------------------------------------------
# imagedev.pl
#
# copyright 2008 H. Carvey, keydet89@yahoo.com
#-----------------------------------------------------------
package imagedev;
use strict;
my %config = (hive => "System",
osmask => 22,
hasShortDescr => 1,
hasDescr => 0,
hasRefs => 0,
version => 20080730);
sub getConfig{return %config}
sub getShortDescr {
return " -- ";
}
sub getDescr{}
sub getRefs {}
sub getHive {return $config{hive};}
sub getVersion {return $config{version};}
my $VERSION = getVersion();
sub pluginmain {
my $class = shift;
my $hive = shift;
::logMsg("Launching imagedev v.".$VERSION);
::rptMsg("imagedev v.".$VERSION); # banner
::rptMsg("(".getHive().") ".getShortDescr()."\n"); # banner
my $reg = Parse::Win32Registry->new($hive);
my $root_key = $reg->get_root_key;
# Code for System file, getting CurrentControlSet
my $current;
my $ccs;
eval {
my $key_path = 'Select';
my $key;
if ($key = $root_key->get_subkey($key_path)) {
$current = $key->get_value("Current")->get_data();
$ccs = "ControlSet00".$current;
}
};
if ($@) {
::rptMsg("Problem locating proper controlset: $@");
return;
}
my $key_path = $ccs."\\Control\\Class\\{6BDD1FC6-810F-11D0-BEC7-08002BE2092F}";
my $key;
if ($key = $root_key->get_subkey($key_path)) {
::rptMsg("imagedev");
::rptMsg($key_path);
# ::rptMsg("LastWrite Time ".gmtime($key->get_timestamp())." (UTC)");
::rptMsg("");
my @sk = $key->get_list_of_subkeys();
if (scalar(@sk) > 0) {
::rptMsg("Still Image Capture Devices");
foreach my $s (@sk) {
my $name = $s->get_name();
next unless ($name =~ m/^\d{4}$/);
my $friendly;
eval {
$friendly = $s->get_value("FriendlyName")->get_data();
::rptMsg(" ".$friendly);
};
if ($@) {
::logMsg("Error getting device FriendlyName in imagedev: ".$@);
}
}
}
else {
::rptMsg($key_path." has no subkeys.");
}
}
else {
::rptMsg($key_path." not found.");
::logMsg($key_path." not found.");
}
}
1; | raman-bt/autopsy | RecentActivity/release/rr-full/plugins/imagedev.pl | Perl | apache-2.0 | 2,227 |
#
# 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 storage::netapp::snmp::mode::listfilesys;
use base qw(centreon::plugins::mode);
use strict;
use warnings;
my $oid_dfFileSys = '.1.3.6.1.4.1.789.1.5.4.1.2';
my $oid_dfType = '.1.3.6.1.4.1.789.1.5.4.1.23';
my $oid_dfKBytesTotal = '.1.3.6.1.4.1.789.1.5.4.1.3';
my $oid_df64TotalKBytes = '.1.3.6.1.4.1.789.1.5.4.1.29';
my %map_types = (
1 => 'traditionalVolume',
2 => 'flexibleVolume',
3 => 'aggregate',
4 => 'stripedAggregate',
5 => 'stripedVolume'
);
sub new {
my ($class, %options) = @_;
my $self = $class->SUPER::new(package => __PACKAGE__, %options);
bless $self, $class;
$self->{version} = '1.0';
$options{options}->add_options(arguments =>
{
"name:s" => { name => 'name' },
"regexp" => { name => 'use_regexp' },
"type:s" => { name => 'type' },
"skip-total-zero" => { name => 'skip_total_zero' },
});
$self->{filesys_id_selected} = [];
return $self;
}
sub check_options {
my ($self, %options) = @_;
$self->SUPER::init(%options);
}
sub manage_selection {
my ($self, %options) = @_;
$self->{result_names} = $self->{snmp}->get_table(oid => $oid_dfFileSys, nothing_quit => 1);
$self->{result_types} = $self->{snmp}->get_table(oid => $oid_dfType, nothing_quit => 1);
foreach my $oid ($self->{snmp}->oid_lex_sort(keys %{$self->{result_names}})) {
next if ($oid !~ /\.([0-9]+)$/);
my $instance = $1;
my $type = $map_types{$self->{result_types}->{$oid_dfType . '.' . $instance}};
# Get all without a name
if (!defined($self->{option_results}->{name})) {
push @{$self->{filesys_id_selected}}, $instance;
next;
}
if (defined($self->{option_results}->{type}) && $type !~ /$self->{option_results}->{type}/i) {
$self->{output}->output_add(long_msg => "Skipping filesys '" . $self->{result_names}->{$oid} . "': no matching filter type");
next;
}
if (!defined($self->{option_results}->{use_regexp}) && $self->{result_names}->{$oid} ne $self->{option_results}->{name}) {
$self->{output}->output_add(long_msg => "Skipping filesys '" . $self->{result_names}->{$oid} . "': no matching filter name");
next;
}
if (defined($self->{option_results}->{use_regexp}) && $self->{result_names}->{$oid} !~ /$self->{option_results}->{name}/) {
$self->{output}->output_add(long_msg => "Skipping filesys '" . $self->{result_names}->{$oid} . "': no matching filter name (regexp)");
next;
}
push @{$self->{filesys_id_selected}}, $instance;
}
}
sub get_additional_information {
my ($self, %options) = @_;
return if (scalar(@{$self->{filesys_id_selected}}) <= 0);
$self->{snmp}->load(oids => [$oid_dfKBytesTotal], instances => $self->{filesys_id_selected});
if (!$self->{snmp}->is_snmpv1()) {
$self->{snmp}->load(oids => [$oid_df64TotalKBytes], instances => $self->{filesys_id_selected});
}
return $self->{snmp}->get_leef();
}
sub run {
my ($self, %options) = @_;
$self->{snmp} = $options{snmp};
$self->manage_selection();
my $result = $self->get_additional_information();
foreach my $instance (sort @{$self->{filesys_id_selected}}) {
my $name = $self->{result_names}->{$oid_dfFileSys . '.' . $instance};
my $type = $self->{result_types}->{$oid_dfType . '.' . $instance};
my $total_size = $result->{$oid_dfKBytesTotal . '.' . $instance} * 1024;
if (defined($result->{$oid_df64TotalKBytes . '.' . $instance}) && $result->{$oid_df64TotalKBytes . '.' . $instance} != 0) {
$total_size = $result->{$oid_df64TotalKBytes . '.' . $instance} * 1024;
}
if (defined($self->{option_results}->{skip_total_zero}) && $total_size == 0) {
$self->{output}->output_add(long_msg => "Skipping filesys '" . $name . "': total size is 0 and option --skip-total-zero is set");
next;
}
$self->{output}->output_add(long_msg => "'" . $name . "' [total_size = $total_size B] [type = " . $map_types{$type} . "]");
}
$self->{output}->output_add(severity => 'OK',
short_msg => 'List filesys:');
$self->{output}->display(nolabel => 1, force_ignore_perfdata => 1, force_long_output => 1);
$self->{output}->exit();
}
sub disco_format {
my ($self, %options) = @_;
$self->{output}->add_disco_format(elements => ['name', 'total', 'type']);
}
sub disco_show {
my ($self, %options) = @_;
$self->{snmp} = $options{snmp};
$self->manage_selection();
my $result = $self->get_additional_information();
foreach my $instance (sort @{$self->{filesys_id_selected}}) {
my $name = $self->{result_names}->{$oid_dfFileSys . '.' . $instance};
my $type = $self->{result_types}->{$oid_dfType . '.' . $instance};
my $total_size = $result->{$oid_dfKBytesTotal . '.' . $instance} * 1024;
if (defined($result->{$oid_df64TotalKBytes . '.' . $instance}) && $result->{$oid_df64TotalKBytes . '.' . $instance} != 0) {
$total_size = $result->{$oid_df64TotalKBytes . '.' . $instance} * 1024;
}
next if (defined($self->{option_results}->{skip_total_zero}) && $total_size == 0);
$self->{output}->add_disco_entry(name => $name,
total => $total_size,
type => $map_types{$type});
}
}
1;
__END__
=head1 MODE
List filesystems (volumes and aggregates also).
=over 8
=item B<--name>
Set the filesystem name.
=item B<--regexp>
Allows to use regexp to filter filesystem name (with option --name).
=item B<--type>
Filter filesystem type (a regexp. Example: 'flexibleVolume|aggregate').
=item B<--skip-total-zero>
Don't display filesys with total equals 0.
=back
=cut
| nichols-356/centreon-plugins | storage/netapp/snmp/mode/listfilesys.pm | Perl | apache-2.0 | 6,933 |
# 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;
package Lucy;
use 5.008003;
our $VERSION = '0.006000';
$VERSION = eval $VERSION;
our $MAJOR_VERSION = 0.006000;
use Clownfish 0.006000;
BEGIN {
die <<"EOF" if $Clownfish::MAJOR_VERSION > 0.006000;
This version of Lucy doesn't support Clownfish $Clownfish::MAJOR_VERSION or
higher. You should downgrade Clownfish or, if possible, upgrade Lucy.
EOF
}
use Exporter 'import';
BEGIN {
our @EXPORT_OK = qw(
STORABLE_freeze
STORABLE_thaw
);
}
# On most UNIX variants, this flag makes DynaLoader pass RTLD_GLOBAL to
# dl_open, so extensions can resolve the needed symbols without explicitly
# linking against the DSO.
sub dl_load_flags { 1 }
BEGIN {
require DynaLoader;
our @ISA = qw( DynaLoader );
# This loads a large number of disparate subs.
bootstrap Lucy '0.6.0';
}
{
package Lucy::Util::IndexFileNames;
our $VERSION = '0.006000';
$VERSION = eval $VERSION;
BEGIN {
push our @ISA, 'Exporter';
our @EXPORT_OK = qw(
extract_gen
latest_snapshot
);
}
}
{
# Temporary back compat.
package Lucy::Object::Obj;
BEGIN { our @ISA = qw( Clownfish::Obj ) }
}
{
package Lucy::Analysis::RegexTokenizer;
our $VERSION = '0.006000';
$VERSION = eval $VERSION;
sub _compile_token_re {qr/$_[0]/}
sub new {
my ( $either, %args ) = @_;
my $token_re = delete $args{token_re};
$args{pattern} = "$token_re" if $token_re;
return $either->_new(%args);
}
}
{
package Lucy::Document::Doc;
our $VERSION = '0.006000';
$VERSION = eval $VERSION;
use Storable (); # Needed by serialize/deserialize.
use Lucy qw( STORABLE_freeze STORABLE_thaw );
use overload
fallback => 1,
'%{}' => \&get_fields;
}
{
package Lucy::Index::DocVector;
our $VERSION = '0.006000';
$VERSION = eval $VERSION;
use Lucy qw( STORABLE_freeze STORABLE_thaw );
}
{
package Lucy::Index::Indexer;
our $VERSION = '0.006000';
$VERSION = eval $VERSION;
sub new {
my ( $either, %args ) = @_;
my $flags = 0;
$flags |= CREATE if delete $args{'create'};
$flags |= TRUNCATE if delete $args{'truncate'};
return $either->_new( %args, flags => $flags );
}
}
{
package Lucy::Index::IndexReader;
our $VERSION = '0.006000';
$VERSION = eval $VERSION;
use Carp;
sub new {
confess(
"IndexReader is an abstract class; use open() instead of new()");
}
sub lexicon {
my $self = shift;
my $lex_reader = $self->fetch("Lucy::Index::LexiconReader");
return $lex_reader->lexicon(@_) if $lex_reader;
return;
}
sub posting_list {
my $self = shift;
my $plist_reader = $self->fetch("Lucy::Index::PostingListReader");
return $plist_reader->posting_list(@_) if $plist_reader;
return;
}
sub offsets { shift->_offsets->to_arrayref }
}
{
package Lucy::Index::Similarity;
our $VERSION = '0.006000';
$VERSION = eval $VERSION;
use Lucy qw( STORABLE_freeze STORABLE_thaw );
}
{
package Lucy::Index::TermVector;
our $VERSION = '0.006000';
$VERSION = eval $VERSION;
use Lucy qw( STORABLE_freeze STORABLE_thaw );
}
{
package Lucy::Search::Compiler;
our $VERSION = '0.006000';
$VERSION = eval $VERSION;
use Carp;
use Scalar::Util qw( blessed );
sub new {
my ( $either, %args ) = @_;
if ( !defined $args{boost} ) {
confess("'parent' is not a Query")
unless ( blessed( $args{parent} )
and $args{parent}->isa("Lucy::Search::Query") );
$args{boost} = $args{parent}->get_boost;
}
return $either->do_new(%args);
}
}
{
package Lucy::Search::MatchDoc;
our $VERSION = '0.006000';
$VERSION = eval $VERSION;
use Lucy qw( STORABLE_freeze STORABLE_thaw );
}
{
package Lucy::Search::Query;
our $VERSION = '0.006000';
$VERSION = eval $VERSION;
use Lucy qw( STORABLE_freeze STORABLE_thaw );
}
{
package Lucy::Search::SortRule;
our $VERSION = '0.006000';
$VERSION = eval $VERSION;
use Carp;
use Lucy qw( STORABLE_freeze STORABLE_thaw );
my %types = (
field => FIELD(),
score => SCORE(),
doc_id => DOC_ID(),
);
sub new {
my ( $either, %args ) = @_;
my $type = delete $args{type} || 'field';
confess("Invalid type: '$type'") unless defined $types{$type};
return $either->_new( %args, type => $types{$type} );
}
}
{
package Lucy::Search::SortSpec;
our $VERSION = '0.006000';
$VERSION = eval $VERSION;
use Lucy qw( STORABLE_freeze STORABLE_thaw );
}
{
package Lucy::Search::TopDocs;
our $VERSION = '0.006000';
$VERSION = eval $VERSION;
use Lucy qw( STORABLE_freeze STORABLE_thaw );
}
{
package Lucy::Object::BitVector;
our $VERSION = '0.006000';
$VERSION = eval $VERSION;
sub to_arrayref { shift->to_array->to_arrayref }
}
{
package Lucy::Store::FileHandle;
our $VERSION = '0.006000';
$VERSION = eval $VERSION;
BEGIN {
push our @ISA, 'Exporter';
our @EXPORT_OK = qw( build_fh_flags );
}
sub build_fh_flags {
my $args = shift;
my $flags = 0;
$flags |= FH_CREATE if delete $args->{create};
$flags |= FH_READ_ONLY if delete $args->{read_only};
$flags |= FH_WRITE_ONLY if delete $args->{write_only};
$flags |= FH_EXCLUSIVE if delete $args->{exclusive};
return $flags;
}
sub open {
my ( $either, %args ) = @_;
$args{flags} ||= 0;
$args{flags} |= build_fh_flags( \%args );
return $either->_open(%args);
}
}
{
package Lucy::Store::FSFileHandle;
our $VERSION = '0.006000';
$VERSION = eval $VERSION;
sub open {
my ( $either, %args ) = @_;
$args{flags} ||= 0;
$args{flags} |= Lucy::Store::FileHandle::build_fh_flags( \%args );
return $either->_open(%args);
}
}
{
package Lucy::Store::RAMFileHandle;
our $VERSION = '0.006000';
$VERSION = eval $VERSION;
sub open {
my ( $either, %args ) = @_;
$args{flags} ||= 0;
$args{flags} |= Lucy::Store::FileHandle::build_fh_flags( \%args );
return $either->_open(%args);
}
}
{
package Lucy::Util::Debug;
our $VERSION = '0.006000';
$VERSION = eval $VERSION;
BEGIN {
push our @ISA, 'Exporter';
our @EXPORT_OK = qw(
DEBUG
DEBUG_PRINT
DEBUG_ENABLED
ASSERT
set_env_cache
num_allocated
num_freed
num_globals
);
}
}
{
package Lucy::Util::StringHelper;
our $VERSION = '0.006000';
$VERSION = eval $VERSION;
BEGIN {
push our @ISA, 'Exporter';
our @EXPORT_OK = qw(
utf8_flag_on
utf8_flag_off
to_base36
utf8ify
utf8_valid
cat_bytes
);
}
}
1;
__END__
| apache/lucy | perl/lib/Lucy.pm | Perl | apache-2.0 | 7,962 |
#!/usr/bin/perl -w
# Copyright (C) 2004 Michael Bell.
# License: GPL version 2
our $iconv = "iconv";
our $QUIET_ARG = 0;
my $po_file = $ARGV[0];
print STDERR "Translation file: $po_file\n";
my $encoding = get_po_encoding ($po_file);
my $command = "$iconv -f $encoding -t UTF-8 $po_file";
print STDERR "Final command: $command\n";
my $ret = `$command`;
print $ret;
# Original code taken from:
#
# The Intltool Message Merger
#
# Copyright (C) 2000, 2003 Free Software Foundation.
# Copyright (C) 2000, 2001 Eazel, Inc
#
# Authors: Maciej Stachowiak <mjs@noisehavoc.org>
# Kenneth Christiansen <kenneth@gnu.org>
# Darin Adler <darin@bentspoon.com>
sub get_po_encoding
{
my ($in_po_file) = @_;
my $encoding = "";
open IN_PO_FILE, $in_po_file or die;
while (<IN_PO_FILE>)
{
## example: "Content-Type: text/plain; charset=ISO-8859-1\n"
if (/Content-Type\:.*charset=([-a-zA-Z0-9]+)\\n/)
{
$encoding = $1;
last;
}
}
close IN_PO_FILE;
if (!$encoding)
{
print STDERR "Warning: no encoding found in $in_po_file. Assuming ISO-8859-1\n" unless $QUIET_ARG;
$encoding = "ISO-8859-1";
}
system ("$iconv -f $encoding -t UTF-8 </dev/null 2>/dev/null");
if ($?) {
$encoding = get_local_charset($encoding);
}
return $encoding
}
| mrscotty/openxpki | core/i18n/convert.pl | Perl | apache-2.0 | 1,387 |
line1=Opcje konfiguracyjne,11
expert=Pozwalaæ na wybór poszczególnych poziomów pracy systemu,1,1-Tak,0-Nie
desc=Wy¶wietlaæ dzia³ania wraz z opisami,1,2,Tak, i pokazuj wszystkie poziomy,1-Tak,0-Nie
order=Wy¶wietlaæ kolejno¶æ bootowania akcji?,1,1-Tak,0-Nie
status_check=Pokazywaæ bie¿±cy stan akcji,1,2-Na stronach indeksowej i akcji,1-Tylko na stronie akcji,0-Nie
sort_mode=Sortuj akcje wed³ug,1,1-Kolejno¶ci bootowania,0-Nazwy
line2=Konfiguracja systemu,11
init_base=Katalog zawieraj±cy podkatalogi poziomów pracy,0
init_dir=Katalog zawieraj±cy nadrzêdne skrypty startowe,0
soft_links=Stosowany rodzaj dowi±zañ do plików poziomów pracy,1,0-Twarde,1-Miêkkie
order_digits=Liczba cyfr okre¶laj±cych kolejno¶æ uruchamiania,0
local_script=Lokalny skrypt poleceñ startowych,3
local_down=Lokalny skrypt poleceñ wy³±czania,3,Brak
reboot_command=Polecenie restartuj±ce system,0
shutdown_command=Polecenie zamykaj±ce system,0
start_stop_msg=System wspomaga komunikaty startowe/zamykaj±ce,1,0-Nie,1-Tak
inittab_id=ID inicjalnego poziomu pracy w inittab-ie,0
daemons_dir=Katalog demonów Caldery,3,Brak
no_chkconfig=U¿yæ polecenie chkconfig do w³±czania akcji?,1,0-Tak,1-Nie
rc_dir=Katalogi skryptów rc FreeBSD,3,Brak
rc_conf=Plik konfiguracyjny FreeBSD,3,Brak
line3=Konfiguracja systemu OSX,11
startup_dirs=Katalogi StartupItems Darwina,0
darwin_setup=Katalog dla indywidualnych StartupItems,0
hostconfig=Plik hostconfig Darwina,0
plist=Nazwa p-listy w katalogu StartupItems,0
| rcuvgd/Webmin22.01.2016 | init/config.info.pl | Perl | bsd-3-clause | 1,486 |
package Moose::Manual::Delegation;
# ABSTRACT: Attribute delegation
=pod
=head1 NAME
Moose::Manual::Delegation - Attribute delegation
=head1 VERSION
version 2.0604
=head1 WHAT IS DELEGATION?
Delegation is a feature that lets you create "proxy" methods that do nothing
more than call some other method on an attribute. This lets you simplify a
complex set of "has-a" relationships and present a single unified API from one
class.
With delegation, consumers of a class don't need to know about all the
objects it contains, reducing the amount of API they need to learn.
Delegations are defined as a mapping between one or more methods
provided by the "real" class (the delegatee), and a set of
corresponding methods in the delegating class. The delegating class
can re-use the method names provided by the delegatee or provide its
own names.
Delegation is also a great way to wrap an existing class, especially a
non-Moose class or one that is somehow hard (or impossible) to
subclass.
=head1 DEFINING A MAPPING
Moose offers a number of options for defining a delegation's mapping,
ranging from simple to complex.
The simplest form is to simply specify a list of methods:
package Website;
use Moose;
has 'uri' => (
is => 'ro',
isa => 'URI',
handles => [qw( host path )],
);
With this definition, we can call C<< $website->host >> and it "just
works". Under the hood, Moose will call C<< $website->uri->host >> for
you. Note that C<$website> is not automatically passed to the C<host>
method; the invocant is C<< $website->uri >>.
We can also define a mapping as a hash reference. This allows you to
rename methods as part of the mapping:
package Website;
use Moose;
has 'uri' => (
is => 'ro',
isa => 'URI',
handles => {
hostname => 'host',
path => 'path',
},
);
In this example, we've created a C<< $website->hostname >> method,
rather than using C<URI.pm>'s name, C<host>.
These two mapping forms are the ones you will use most often. The
remaining methods are a bit more complex.
has 'uri' => (
is => 'ro',
isa => 'URI',
handles => qr/^(?:host|path|query.*)/,
);
This is similar to the array version, except it uses the regex to
match against all the methods provided by the delegatee. In order for
this to work, you must provide an C<isa> parameter for the attribute,
and it must be a class. Moose uses this to introspect the delegatee
class and determine what methods it provides.
You can use a role name as the value of C<handles>:
has 'uri' => (
is => 'ro',
isa => 'URI',
handles => 'HasURI',
);
Moose will introspect the role to determine what methods it provides
and create a mapping for each of those methods.
Finally, you can also provide a sub reference to I<generate> a
mapping. You probably won't need this version often (if ever). See the
L<Moose> docs for more details on exactly how this works.
=head1 NATIVE DELEGATION
Native delegations allow you to delegate to standard Perl data structures as
if they were objects.
has 'queue' => (
traits => ['Array'],
isa => 'ArrayRef[Item]',
default => sub { [ ] },
handles => {
add_item => 'push',
next_item => 'shift',
},
)
The C<Array> trait in the C<traits> parameter tells Moose that you would like
to use the set of Array helpers. Moose will then create C<add_item> and
C<next_item> methods that "just work". Behind the scenes C<add_item> is
something like
sub add_item {
my ($self, @items) = @_;
for my $item (@items) {
$Item_TC->validate($item);
}
push @{ $self->queue }, @items;
}
Moose includes the following traits for native delegation:
=over 4
=item * L<Array|Moose::Meta::Attribute::Native::Trait::Array>
=item * L<Bool|Moose::Meta::Attribute::Native::Trait::Bool>
=item * L<Code|Moose::Meta::Attribute::Native::Trait::Code>
=item * L<Counter|Moose::Meta::Attribute::Native::Trait::Counter>
=item * L<Hash|Moose::Meta::Attribute::Native::Trait::Hash>
=item * L<Number|Moose::Meta::Attribute::Native::Trait::Number>
=item * L<String|Moose::Meta::Attribute::Native::Trait::String>
=back
=head1 CURRYING
Currying allows you to create a method with some pre-set parameters. You can
create a curried delegation method:
package Spider;
use Moose;
has request => (
is => 'ro'
isa => 'HTTP::Request',
handles => {
set_user_agent => [ header => 'UserAgent' ],
},
)
With this definition, calling C<< $spider->set_user_agent('MyClient') >> will
call C<< $spider->request->header('UserAgent', 'MyClient') >> behind the
scenes.
Note that with currying, the currying always starts with the first parameter to
a method (C<$_[0]>). Any arguments you pass to the delegation come after the
curried arguments.
=head1 MISSING ATTRIBUTES
It is perfectly valid to delegate methods to an attribute which is not
required or can be undefined. When a delegated method is called, Moose
will throw a runtime error if the attribute does not contain an
object.
=head1 AUTHOR
Moose is maintained by the Moose Cabal, along with the help of many contributors. See L<Moose/CABAL> and L<Moose/CONTRIBUTORS> for details.
=head1 COPYRIGHT AND LICENSE
This software is copyright (c) 2012 by Infinity Interactive, Inc..
This is free software; you can redistribute it and/or modify it under
the same terms as the Perl 5 programming language system itself.
=cut
__END__
| liuyangning/WX_web | xampp/perl/vendor/lib/Moose/Manual/Delegation.pod | Perl | mit | 5,592 |
#!/usr/bin/env perl
# ====================================================================
# Written by Andy Polyakov <appro@openssl.org> for the OpenSSL
# project. The module is, however, dual licensed under OpenSSL and
# CRYPTOGAMS licenses depending on where you obtain it. For further
# details see http://www.openssl.org/~appro/cryptogams/.
# ====================================================================
# Multi-buffer AES-NI procedures process several independent buffers
# in parallel by interleaving independent instructions.
#
# Cycles per byte for interleave factor 4:
#
# asymptotic measured
# ---------------------------
# Westmere 5.00/4=1.25 5.13/4=1.28
# Atom 15.0/4=3.75 ?15.7/4=3.93
# Sandy Bridge 5.06/4=1.27 5.18/4=1.29
# Ivy Bridge 5.06/4=1.27 5.14/4=1.29
# Haswell 4.44/4=1.11 4.44/4=1.11
# Bulldozer 5.75/4=1.44 5.76/4=1.44
#
# Cycles per byte for interleave factor 8 (not implemented for
# pre-AVX processors, where higher interleave factor incidentally
# doesn't result in improvement):
#
# asymptotic measured
# ---------------------------
# Sandy Bridge 5.06/8=0.64 7.10/8=0.89(*)
# Ivy Bridge 5.06/8=0.64 7.14/8=0.89(*)
# Haswell 5.00/8=0.63 5.00/8=0.63
# Bulldozer 5.75/8=0.72 5.77/8=0.72
#
# (*) Sandy/Ivy Bridge are known to handle high interleave factors
# suboptimally;
$flavour = shift;
$output = shift;
if ($flavour =~ /\./) { $output = $flavour; undef $flavour; }
$win64=0; $win64=1 if ($flavour =~ /[nm]asm|mingw64/ || $output =~ /\.asm$/);
$0 =~ m/(.*[\/\\])[^\/\\]+$/; $dir=$1;
( $xlate="${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";
$avx=0;
if (`$ENV{CC} -Wa,-v -c -o /dev/null -x assembler /dev/null 2>&1`
=~ /GNU assembler version ([2-9]\.[0-9]+)/) {
$avx = ($1>=2.19) + ($1>=2.22);
}
if (!$avx && $win64 && ($flavour =~ /nasm/ || $ENV{ASM} =~ /nasm/) &&
`nasm -v 2>&1` =~ /NASM version ([2-9]\.[0-9]+)/) {
$avx = ($1>=2.09) + ($1>=2.10);
}
if (!$avx && $win64 && ($flavour =~ /masm/ || $ENV{ASM} =~ /ml64/) &&
`ml64 2>&1` =~ /Version ([0-9]+)\./) {
$avx = ($1>=10) + ($1>=11);
}
if (!$avx && `$ENV{CC} -v 2>&1` =~ /((?:^clang|LLVM) version|based on LLVM) ([3-9]\.[0-9]+)/) {
$avx = ($2>=3.0) + ($2>3.0);
}
open OUT,"| \"$^X\" $xlate $flavour $output";
*STDOUT=*OUT;
# void aesni_multi_cbc_encrypt (
# struct { void *inp,*out; int blocks; double iv[2]; } inp[8];
# const AES_KEY *key,
# int num); /* 1 or 2 */
#
$inp="%rdi"; # 1st arg
$key="%rsi"; # 2nd arg
$num="%edx";
@inptr=map("%r$_",(8..11));
@outptr=map("%r$_",(12..15));
($rndkey0,$rndkey1)=("%xmm0","%xmm1");
@out=map("%xmm$_",(2..5));
@inp=map("%xmm$_",(6..9));
($counters,$mask,$zero)=map("%xmm$_",(10..12));
($rounds,$one,$sink,$offset)=("%eax","%ecx","%rbp","%rbx");
$code.=<<___;
.text
.extern OPENSSL_ia32cap_P
.globl aesni_multi_cbc_encrypt
.type aesni_multi_cbc_encrypt,\@function,3
.align 32
aesni_multi_cbc_encrypt:
___
$code.=<<___ if ($avx);
cmp \$2,$num
jb .Lenc_non_avx
mov OPENSSL_ia32cap_P+4(%rip),%ecx
test \$`1<<28`,%ecx # AVX bit
jnz _avx_cbc_enc_shortcut
jmp .Lenc_non_avx
.align 16
.Lenc_non_avx:
___
$code.=<<___;
mov %rsp,%rax
push %rbx
push %rbp
push %r12
push %r13
push %r14
push %r15
___
$code.=<<___ if ($win64);
lea -0xa8(%rsp),%rsp
movaps %xmm6,(%rsp)
movaps %xmm7,0x10(%rsp)
movaps %xmm8,0x20(%rsp)
movaps %xmm9,0x30(%rsp)
movaps %xmm10,0x40(%rsp)
movaps %xmm11,0x50(%rsp)
movaps %xmm12,0x60(%rsp)
movaps %xmm13,-0x68(%rax) # not used, saved to share se_handler
movaps %xmm14,-0x58(%rax)
movaps %xmm15,-0x48(%rax)
___
$code.=<<___;
# stack layout
#
# +0 output sink
# +16 input sink [original %rsp and $num]
# +32 counters
sub \$48,%rsp
and \$-64,%rsp
mov %rax,16(%rsp) # original %rsp
.Lenc4x_body:
movdqu ($key),$zero # 0-round key
lea 0x78($key),$key # size optimization
lea 40*2($inp),$inp
.Lenc4x_loop_grande:
mov $num,24(%rsp) # original $num
xor $num,$num
___
for($i=0;$i<4;$i++) {
$code.=<<___;
mov `40*$i+16-40*2`($inp),$one # borrow $one for number of blocks
mov `40*$i+0-40*2`($inp),@inptr[$i]
cmp $num,$one
mov `40*$i+8-40*2`($inp),@outptr[$i]
cmovg $one,$num # find maximum
test $one,$one
movdqu `40*$i+24-40*2`($inp),@out[$i] # load IV
mov $one,`32+4*$i`(%rsp) # initialize counters
cmovle %rsp,@inptr[$i] # cancel input
___
}
$code.=<<___;
test $num,$num
jz .Lenc4x_done
movups 0x10-0x78($key),$rndkey1
pxor $zero,@out[0]
movups 0x20-0x78($key),$rndkey0
pxor $zero,@out[1]
mov 0xf0-0x78($key),$rounds
pxor $zero,@out[2]
movdqu (@inptr[0]),@inp[0] # load inputs
pxor $zero,@out[3]
movdqu (@inptr[1]),@inp[1]
pxor @inp[0],@out[0]
movdqu (@inptr[2]),@inp[2]
pxor @inp[1],@out[1]
movdqu (@inptr[3]),@inp[3]
pxor @inp[2],@out[2]
pxor @inp[3],@out[3]
movdqa 32(%rsp),$counters # load counters
xor $offset,$offset
jmp .Loop_enc4x
.align 32
.Loop_enc4x:
add \$16,$offset
lea 16(%rsp),$sink # sink pointer
mov \$1,$one # constant of 1
sub $offset,$sink
aesenc $rndkey1,@out[0]
prefetcht0 31(@inptr[0],$offset) # prefetch input
prefetcht0 31(@inptr[1],$offset)
aesenc $rndkey1,@out[1]
prefetcht0 31(@inptr[2],$offset)
prefetcht0 31(@inptr[2],$offset)
aesenc $rndkey1,@out[2]
aesenc $rndkey1,@out[3]
movups 0x30-0x78($key),$rndkey1
___
for($i=0;$i<4;$i++) {
my $rndkey = ($i&1) ? $rndkey1 : $rndkey0;
$code.=<<___;
cmp `32+4*$i`(%rsp),$one
aesenc $rndkey,@out[0]
aesenc $rndkey,@out[1]
aesenc $rndkey,@out[2]
cmovge $sink,@inptr[$i] # cancel input
cmovg $sink,@outptr[$i] # sink output
aesenc $rndkey,@out[3]
movups `0x40+16*$i-0x78`($key),$rndkey
___
}
$code.=<<___;
movdqa $counters,$mask
aesenc $rndkey0,@out[0]
prefetcht0 15(@outptr[0],$offset) # prefetch output
prefetcht0 15(@outptr[1],$offset)
aesenc $rndkey0,@out[1]
prefetcht0 15(@outptr[2],$offset)
prefetcht0 15(@outptr[3],$offset)
aesenc $rndkey0,@out[2]
aesenc $rndkey0,@out[3]
movups 0x80-0x78($key),$rndkey0
pxor $zero,$zero
aesenc $rndkey1,@out[0]
pcmpgtd $zero,$mask
movdqu -0x78($key),$zero # reload 0-round key
aesenc $rndkey1,@out[1]
paddd $mask,$counters # decrement counters
movdqa $counters,32(%rsp) # update counters
aesenc $rndkey1,@out[2]
aesenc $rndkey1,@out[3]
movups 0x90-0x78($key),$rndkey1
cmp \$11,$rounds
aesenc $rndkey0,@out[0]
aesenc $rndkey0,@out[1]
aesenc $rndkey0,@out[2]
aesenc $rndkey0,@out[3]
movups 0xa0-0x78($key),$rndkey0
jb .Lenc4x_tail
aesenc $rndkey1,@out[0]
aesenc $rndkey1,@out[1]
aesenc $rndkey1,@out[2]
aesenc $rndkey1,@out[3]
movups 0xb0-0x78($key),$rndkey1
aesenc $rndkey0,@out[0]
aesenc $rndkey0,@out[1]
aesenc $rndkey0,@out[2]
aesenc $rndkey0,@out[3]
movups 0xc0-0x78($key),$rndkey0
je .Lenc4x_tail
aesenc $rndkey1,@out[0]
aesenc $rndkey1,@out[1]
aesenc $rndkey1,@out[2]
aesenc $rndkey1,@out[3]
movups 0xd0-0x78($key),$rndkey1
aesenc $rndkey0,@out[0]
aesenc $rndkey0,@out[1]
aesenc $rndkey0,@out[2]
aesenc $rndkey0,@out[3]
movups 0xe0-0x78($key),$rndkey0
jmp .Lenc4x_tail
.align 32
.Lenc4x_tail:
aesenc $rndkey1,@out[0]
aesenc $rndkey1,@out[1]
aesenc $rndkey1,@out[2]
aesenc $rndkey1,@out[3]
movdqu (@inptr[0],$offset),@inp[0]
movdqu 0x10-0x78($key),$rndkey1
aesenclast $rndkey0,@out[0]
movdqu (@inptr[1],$offset),@inp[1]
pxor $zero,@inp[0]
aesenclast $rndkey0,@out[1]
movdqu (@inptr[2],$offset),@inp[2]
pxor $zero,@inp[1]
aesenclast $rndkey0,@out[2]
movdqu (@inptr[3],$offset),@inp[3]
pxor $zero,@inp[2]
aesenclast $rndkey0,@out[3]
movdqu 0x20-0x78($key),$rndkey0
pxor $zero,@inp[3]
movups @out[0],-16(@outptr[0],$offset)
pxor @inp[0],@out[0]
movups @out[1],-16(@outptr[1],$offset)
pxor @inp[1],@out[1]
movups @out[2],-16(@outptr[2],$offset)
pxor @inp[2],@out[2]
movups @out[3],-16(@outptr[3],$offset)
pxor @inp[3],@out[3]
dec $num
jnz .Loop_enc4x
mov 16(%rsp),%rax # original %rsp
mov 24(%rsp),$num
#pxor @inp[0],@out[0]
#pxor @inp[1],@out[1]
#movdqu @out[0],`40*0+24-40*2`($inp) # output iv FIX ME!
#pxor @inp[2],@out[2]
#movdqu @out[1],`40*1+24-40*2`($inp)
#pxor @inp[3],@out[3]
#movdqu @out[2],`40*2+24-40*2`($inp) # won't fix, let caller
#movdqu @out[3],`40*3+24-40*2`($inp) # figure this out...
lea `40*4`($inp),$inp
dec $num
jnz .Lenc4x_loop_grande
.Lenc4x_done:
___
$code.=<<___ if ($win64);
movaps -0xd8(%rax),%xmm6
movaps -0xc8(%rax),%xmm7
movaps -0xb8(%rax),%xmm8
movaps -0xa8(%rax),%xmm9
movaps -0x98(%rax),%xmm10
movaps -0x88(%rax),%xmm11
movaps -0x78(%rax),%xmm12
#movaps -0x68(%rax),%xmm13
#movaps -0x58(%rax),%xmm14
#movaps -0x48(%rax),%xmm15
___
$code.=<<___;
mov -48(%rax),%r15
mov -40(%rax),%r14
mov -32(%rax),%r13
mov -24(%rax),%r12
mov -16(%rax),%rbp
mov -8(%rax),%rbx
lea (%rax),%rsp
.Lenc4x_epilogue:
ret
.size aesni_multi_cbc_encrypt,.-aesni_multi_cbc_encrypt
.globl aesni_multi_cbc_decrypt
.type aesni_multi_cbc_decrypt,\@function,3
.align 32
aesni_multi_cbc_decrypt:
___
$code.=<<___ if ($avx);
cmp \$2,$num
jb .Ldec_non_avx
mov OPENSSL_ia32cap_P+4(%rip),%ecx
test \$`1<<28`,%ecx # AVX bit
jnz _avx_cbc_dec_shortcut
jmp .Ldec_non_avx
.align 16
.Ldec_non_avx:
___
$code.=<<___;
mov %rsp,%rax
push %rbx
push %rbp
push %r12
push %r13
push %r14
push %r15
___
$code.=<<___ if ($win64);
lea -0xa8(%rsp),%rsp
movaps %xmm6,(%rsp)
movaps %xmm7,0x10(%rsp)
movaps %xmm8,0x20(%rsp)
movaps %xmm9,0x30(%rsp)
movaps %xmm10,0x40(%rsp)
movaps %xmm11,0x50(%rsp)
movaps %xmm12,0x60(%rsp)
movaps %xmm13,-0x68(%rax) # not used, saved to share se_handler
movaps %xmm14,-0x58(%rax)
movaps %xmm15,-0x48(%rax)
___
$code.=<<___;
# stack layout
#
# +0 output sink
# +16 input sink [original %rsp and $num]
# +32 counters
sub \$48,%rsp
and \$-64,%rsp
mov %rax,16(%rsp) # original %rsp
.Ldec4x_body:
movdqu ($key),$zero # 0-round key
lea 0x78($key),$key # size optimization
lea 40*2($inp),$inp
.Ldec4x_loop_grande:
mov $num,24(%rsp) # original $num
xor $num,$num
___
for($i=0;$i<4;$i++) {
$code.=<<___;
mov `40*$i+16-40*2`($inp),$one # borrow $one for number of blocks
mov `40*$i+0-40*2`($inp),@inptr[$i]
cmp $num,$one
mov `40*$i+8-40*2`($inp),@outptr[$i]
cmovg $one,$num # find maximum
test $one,$one
movdqu `40*$i+24-40*2`($inp),@inp[$i] # load IV
mov $one,`32+4*$i`(%rsp) # initialize counters
cmovle %rsp,@inptr[$i] # cancel input
___
}
$code.=<<___;
test $num,$num
jz .Ldec4x_done
movups 0x10-0x78($key),$rndkey1
movups 0x20-0x78($key),$rndkey0
mov 0xf0-0x78($key),$rounds
movdqu (@inptr[0]),@out[0] # load inputs
movdqu (@inptr[1]),@out[1]
pxor $zero,@out[0]
movdqu (@inptr[2]),@out[2]
pxor $zero,@out[1]
movdqu (@inptr[3]),@out[3]
pxor $zero,@out[2]
pxor $zero,@out[3]
movdqa 32(%rsp),$counters # load counters
xor $offset,$offset
jmp .Loop_dec4x
.align 32
.Loop_dec4x:
add \$16,$offset
lea 16(%rsp),$sink # sink pointer
mov \$1,$one # constant of 1
sub $offset,$sink
aesdec $rndkey1,@out[0]
prefetcht0 31(@inptr[0],$offset) # prefetch input
prefetcht0 31(@inptr[1],$offset)
aesdec $rndkey1,@out[1]
prefetcht0 31(@inptr[2],$offset)
prefetcht0 31(@inptr[3],$offset)
aesdec $rndkey1,@out[2]
aesdec $rndkey1,@out[3]
movups 0x30-0x78($key),$rndkey1
___
for($i=0;$i<4;$i++) {
my $rndkey = ($i&1) ? $rndkey1 : $rndkey0;
$code.=<<___;
cmp `32+4*$i`(%rsp),$one
aesdec $rndkey,@out[0]
aesdec $rndkey,@out[1]
aesdec $rndkey,@out[2]
cmovge $sink,@inptr[$i] # cancel input
cmovg $sink,@outptr[$i] # sink output
aesdec $rndkey,@out[3]
movups `0x40+16*$i-0x78`($key),$rndkey
___
}
$code.=<<___;
movdqa $counters,$mask
aesdec $rndkey0,@out[0]
prefetcht0 15(@outptr[0],$offset) # prefetch output
prefetcht0 15(@outptr[1],$offset)
aesdec $rndkey0,@out[1]
prefetcht0 15(@outptr[2],$offset)
prefetcht0 15(@outptr[3],$offset)
aesdec $rndkey0,@out[2]
aesdec $rndkey0,@out[3]
movups 0x80-0x78($key),$rndkey0
pxor $zero,$zero
aesdec $rndkey1,@out[0]
pcmpgtd $zero,$mask
movdqu -0x78($key),$zero # reload 0-round key
aesdec $rndkey1,@out[1]
paddd $mask,$counters # decrement counters
movdqa $counters,32(%rsp) # update counters
aesdec $rndkey1,@out[2]
aesdec $rndkey1,@out[3]
movups 0x90-0x78($key),$rndkey1
cmp \$11,$rounds
aesdec $rndkey0,@out[0]
aesdec $rndkey0,@out[1]
aesdec $rndkey0,@out[2]
aesdec $rndkey0,@out[3]
movups 0xa0-0x78($key),$rndkey0
jb .Ldec4x_tail
aesdec $rndkey1,@out[0]
aesdec $rndkey1,@out[1]
aesdec $rndkey1,@out[2]
aesdec $rndkey1,@out[3]
movups 0xb0-0x78($key),$rndkey1
aesdec $rndkey0,@out[0]
aesdec $rndkey0,@out[1]
aesdec $rndkey0,@out[2]
aesdec $rndkey0,@out[3]
movups 0xc0-0x78($key),$rndkey0
je .Ldec4x_tail
aesdec $rndkey1,@out[0]
aesdec $rndkey1,@out[1]
aesdec $rndkey1,@out[2]
aesdec $rndkey1,@out[3]
movups 0xd0-0x78($key),$rndkey1
aesdec $rndkey0,@out[0]
aesdec $rndkey0,@out[1]
aesdec $rndkey0,@out[2]
aesdec $rndkey0,@out[3]
movups 0xe0-0x78($key),$rndkey0
jmp .Ldec4x_tail
.align 32
.Ldec4x_tail:
aesdec $rndkey1,@out[0]
aesdec $rndkey1,@out[1]
aesdec $rndkey1,@out[2]
pxor $rndkey0,@inp[0]
pxor $rndkey0,@inp[1]
aesdec $rndkey1,@out[3]
movdqu 0x10-0x78($key),$rndkey1
pxor $rndkey0,@inp[2]
pxor $rndkey0,@inp[3]
movdqu 0x20-0x78($key),$rndkey0
aesdeclast @inp[0],@out[0]
aesdeclast @inp[1],@out[1]
movdqu -16(@inptr[0],$offset),@inp[0] # load next IV
movdqu -16(@inptr[1],$offset),@inp[1]
aesdeclast @inp[2],@out[2]
aesdeclast @inp[3],@out[3]
movdqu -16(@inptr[2],$offset),@inp[2]
movdqu -16(@inptr[3],$offset),@inp[3]
movups @out[0],-16(@outptr[0],$offset)
movdqu (@inptr[0],$offset),@out[0]
movups @out[1],-16(@outptr[1],$offset)
movdqu (@inptr[1],$offset),@out[1]
pxor $zero,@out[0]
movups @out[2],-16(@outptr[2],$offset)
movdqu (@inptr[2],$offset),@out[2]
pxor $zero,@out[1]
movups @out[3],-16(@outptr[3],$offset)
movdqu (@inptr[3],$offset),@out[3]
pxor $zero,@out[2]
pxor $zero,@out[3]
dec $num
jnz .Loop_dec4x
mov 16(%rsp),%rax # original %rsp
mov 24(%rsp),$num
lea `40*4`($inp),$inp
dec $num
jnz .Ldec4x_loop_grande
.Ldec4x_done:
___
$code.=<<___ if ($win64);
movaps -0xd8(%rax),%xmm6
movaps -0xc8(%rax),%xmm7
movaps -0xb8(%rax),%xmm8
movaps -0xa8(%rax),%xmm9
movaps -0x98(%rax),%xmm10
movaps -0x88(%rax),%xmm11
movaps -0x78(%rax),%xmm12
#movaps -0x68(%rax),%xmm13
#movaps -0x58(%rax),%xmm14
#movaps -0x48(%rax),%xmm15
___
$code.=<<___;
mov -48(%rax),%r15
mov -40(%rax),%r14
mov -32(%rax),%r13
mov -24(%rax),%r12
mov -16(%rax),%rbp
mov -8(%rax),%rbx
lea (%rax),%rsp
.Ldec4x_epilogue:
ret
.size aesni_multi_cbc_decrypt,.-aesni_multi_cbc_decrypt
___
if ($avx) {{{
my @ptr=map("%r$_",(8..15));
my $offload=$sink;
my @out=map("%xmm$_",(2..9));
my @inp=map("%xmm$_",(10..13));
my ($counters,$zero)=("%xmm14","%xmm15");
$code.=<<___;
.type aesni_multi_cbc_encrypt_avx,\@function,3
.align 32
aesni_multi_cbc_encrypt_avx:
_avx_cbc_enc_shortcut:
mov %rsp,%rax
push %rbx
push %rbp
push %r12
push %r13
push %r14
push %r15
___
$code.=<<___ if ($win64);
lea -0xa8(%rsp),%rsp
movaps %xmm6,(%rsp)
movaps %xmm7,0x10(%rsp)
movaps %xmm8,0x20(%rsp)
movaps %xmm9,0x30(%rsp)
movaps %xmm10,0x40(%rsp)
movaps %xmm11,0x50(%rsp)
movaps %xmm12,-0x78(%rax)
movaps %xmm13,-0x68(%rax)
movaps %xmm14,-0x58(%rax)
movaps %xmm15,-0x48(%rax)
___
$code.=<<___;
# stack layout
#
# +0 output sink
# +16 input sink [original %rsp and $num]
# +32 counters
# +64 distances between inputs and outputs
# +128 off-load area for @inp[0..3]
sub \$192,%rsp
and \$-128,%rsp
mov %rax,16(%rsp) # original %rsp
.Lenc8x_body:
vzeroupper
vmovdqu ($key),$zero # 0-round key
lea 0x78($key),$key # size optimization
lea 40*4($inp),$inp
shr \$1,$num
.Lenc8x_loop_grande:
#mov $num,24(%rsp) # original $num
xor $num,$num
___
for($i=0;$i<8;$i++) {
my $temp = $i ? $offload : $offset;
$code.=<<___;
mov `40*$i+16-40*4`($inp),$one # borrow $one for number of blocks
mov `40*$i+0-40*4`($inp),@ptr[$i] # input pointer
cmp $num,$one
mov `40*$i+8-40*4`($inp),$temp # output pointer
cmovg $one,$num # find maximum
test $one,$one
vmovdqu `40*$i+24-40*4`($inp),@out[$i] # load IV
mov $one,`32+4*$i`(%rsp) # initialize counters
cmovle %rsp,@ptr[$i] # cancel input
sub @ptr[$i],$temp # distance between input and output
mov $temp,`64+8*$i`(%rsp) # initialize distances
___
}
$code.=<<___;
test $num,$num
jz .Lenc8x_done
vmovups 0x10-0x78($key),$rndkey1
vmovups 0x20-0x78($key),$rndkey0
mov 0xf0-0x78($key),$rounds
vpxor (@ptr[0]),$zero,@inp[0] # load inputs and xor with 0-round
lea 128(%rsp),$offload # offload area
vpxor (@ptr[1]),$zero,@inp[1]
vpxor (@ptr[2]),$zero,@inp[2]
vpxor (@ptr[3]),$zero,@inp[3]
vpxor @inp[0],@out[0],@out[0]
vpxor (@ptr[4]),$zero,@inp[0]
vpxor @inp[1],@out[1],@out[1]
vpxor (@ptr[5]),$zero,@inp[1]
vpxor @inp[2],@out[2],@out[2]
vpxor (@ptr[6]),$zero,@inp[2]
vpxor @inp[3],@out[3],@out[3]
vpxor (@ptr[7]),$zero,@inp[3]
vpxor @inp[0],@out[4],@out[4]
mov \$1,$one # constant of 1
vpxor @inp[1],@out[5],@out[5]
vpxor @inp[2],@out[6],@out[6]
vpxor @inp[3],@out[7],@out[7]
jmp .Loop_enc8x
.align 32
.Loop_enc8x:
___
for($i=0;$i<8;$i++) {
my $rndkey=($i&1)?$rndkey0:$rndkey1;
$code.=<<___;
vaesenc $rndkey,@out[0],@out[0]
cmp 32+4*$i(%rsp),$one
___
$code.=<<___ if ($i);
mov 64+8*$i(%rsp),$offset
___
$code.=<<___;
vaesenc $rndkey,@out[1],@out[1]
prefetcht0 31(@ptr[$i]) # prefetch input
vaesenc $rndkey,@out[2],@out[2]
___
$code.=<<___ if ($i>1);
prefetcht0 15(@ptr[$i-2]) # prefetch output
___
$code.=<<___;
vaesenc $rndkey,@out[3],@out[3]
lea (@ptr[$i],$offset),$offset
cmovge %rsp,@ptr[$i] # cancel input
vaesenc $rndkey,@out[4],@out[4]
cmovg %rsp,$offset # sink output
vaesenc $rndkey,@out[5],@out[5]
sub @ptr[$i],$offset
vaesenc $rndkey,@out[6],@out[6]
vpxor 16(@ptr[$i]),$zero,@inp[$i%4] # load input and xor with 0-round
mov $offset,64+8*$i(%rsp)
vaesenc $rndkey,@out[7],@out[7]
vmovups `16*(3+$i)-0x78`($key),$rndkey
lea 16(@ptr[$i],$offset),@ptr[$i] # switch to output
___
$code.=<<___ if ($i<4)
vmovdqu @inp[$i%4],`16*$i`($offload) # off-load
___
}
$code.=<<___;
vmovdqu 32(%rsp),$counters
prefetcht0 15(@ptr[$i-2]) # prefetch output
prefetcht0 15(@ptr[$i-1])
cmp \$11,$rounds
jb .Lenc8x_tail
vaesenc $rndkey1,@out[0],@out[0]
vaesenc $rndkey1,@out[1],@out[1]
vaesenc $rndkey1,@out[2],@out[2]
vaesenc $rndkey1,@out[3],@out[3]
vaesenc $rndkey1,@out[4],@out[4]
vaesenc $rndkey1,@out[5],@out[5]
vaesenc $rndkey1,@out[6],@out[6]
vaesenc $rndkey1,@out[7],@out[7]
vmovups 0xb0-0x78($key),$rndkey1
vaesenc $rndkey0,@out[0],@out[0]
vaesenc $rndkey0,@out[1],@out[1]
vaesenc $rndkey0,@out[2],@out[2]
vaesenc $rndkey0,@out[3],@out[3]
vaesenc $rndkey0,@out[4],@out[4]
vaesenc $rndkey0,@out[5],@out[5]
vaesenc $rndkey0,@out[6],@out[6]
vaesenc $rndkey0,@out[7],@out[7]
vmovups 0xc0-0x78($key),$rndkey0
je .Lenc8x_tail
vaesenc $rndkey1,@out[0],@out[0]
vaesenc $rndkey1,@out[1],@out[1]
vaesenc $rndkey1,@out[2],@out[2]
vaesenc $rndkey1,@out[3],@out[3]
vaesenc $rndkey1,@out[4],@out[4]
vaesenc $rndkey1,@out[5],@out[5]
vaesenc $rndkey1,@out[6],@out[6]
vaesenc $rndkey1,@out[7],@out[7]
vmovups 0xd0-0x78($key),$rndkey1
vaesenc $rndkey0,@out[0],@out[0]
vaesenc $rndkey0,@out[1],@out[1]
vaesenc $rndkey0,@out[2],@out[2]
vaesenc $rndkey0,@out[3],@out[3]
vaesenc $rndkey0,@out[4],@out[4]
vaesenc $rndkey0,@out[5],@out[5]
vaesenc $rndkey0,@out[6],@out[6]
vaesenc $rndkey0,@out[7],@out[7]
vmovups 0xe0-0x78($key),$rndkey0
.Lenc8x_tail:
vaesenc $rndkey1,@out[0],@out[0]
vpxor $zero,$zero,$zero
vaesenc $rndkey1,@out[1],@out[1]
vaesenc $rndkey1,@out[2],@out[2]
vpcmpgtd $zero,$counters,$zero
vaesenc $rndkey1,@out[3],@out[3]
vaesenc $rndkey1,@out[4],@out[4]
vpaddd $counters,$zero,$zero # decrement counters
vmovdqu 48(%rsp),$counters
vaesenc $rndkey1,@out[5],@out[5]
mov 64(%rsp),$offset # pre-load 1st offset
vaesenc $rndkey1,@out[6],@out[6]
vaesenc $rndkey1,@out[7],@out[7]
vmovups 0x10-0x78($key),$rndkey1
vaesenclast $rndkey0,@out[0],@out[0]
vmovdqa $zero,32(%rsp) # update counters
vpxor $zero,$zero,$zero
vaesenclast $rndkey0,@out[1],@out[1]
vaesenclast $rndkey0,@out[2],@out[2]
vpcmpgtd $zero,$counters,$zero
vaesenclast $rndkey0,@out[3],@out[3]
vaesenclast $rndkey0,@out[4],@out[4]
vpaddd $zero,$counters,$counters # decrement counters
vmovdqu -0x78($key),$zero # 0-round
vaesenclast $rndkey0,@out[5],@out[5]
vaesenclast $rndkey0,@out[6],@out[6]
vmovdqa $counters,48(%rsp) # update counters
vaesenclast $rndkey0,@out[7],@out[7]
vmovups 0x20-0x78($key),$rndkey0
vmovups @out[0],-16(@ptr[0]) # write output
sub $offset,@ptr[0] # switch to input
vpxor 0x00($offload),@out[0],@out[0]
vmovups @out[1],-16(@ptr[1])
sub `64+1*8`(%rsp),@ptr[1]
vpxor 0x10($offload),@out[1],@out[1]
vmovups @out[2],-16(@ptr[2])
sub `64+2*8`(%rsp),@ptr[2]
vpxor 0x20($offload),@out[2],@out[2]
vmovups @out[3],-16(@ptr[3])
sub `64+3*8`(%rsp),@ptr[3]
vpxor 0x30($offload),@out[3],@out[3]
vmovups @out[4],-16(@ptr[4])
sub `64+4*8`(%rsp),@ptr[4]
vpxor @inp[0],@out[4],@out[4]
vmovups @out[5],-16(@ptr[5])
sub `64+5*8`(%rsp),@ptr[5]
vpxor @inp[1],@out[5],@out[5]
vmovups @out[6],-16(@ptr[6])
sub `64+6*8`(%rsp),@ptr[6]
vpxor @inp[2],@out[6],@out[6]
vmovups @out[7],-16(@ptr[7])
sub `64+7*8`(%rsp),@ptr[7]
vpxor @inp[3],@out[7],@out[7]
dec $num
jnz .Loop_enc8x
mov 16(%rsp),%rax # original %rsp
#mov 24(%rsp),$num
#lea `40*8`($inp),$inp
#dec $num
#jnz .Lenc8x_loop_grande
.Lenc8x_done:
vzeroupper
___
$code.=<<___ if ($win64);
movaps -0xd8(%rax),%xmm6
movaps -0xc8(%rax),%xmm7
movaps -0xb8(%rax),%xmm8
movaps -0xa8(%rax),%xmm9
movaps -0x98(%rax),%xmm10
movaps -0x88(%rax),%xmm11
movaps -0x78(%rax),%xmm12
movaps -0x68(%rax),%xmm13
movaps -0x58(%rax),%xmm14
movaps -0x48(%rax),%xmm15
___
$code.=<<___;
mov -48(%rax),%r15
mov -40(%rax),%r14
mov -32(%rax),%r13
mov -24(%rax),%r12
mov -16(%rax),%rbp
mov -8(%rax),%rbx
lea (%rax),%rsp
.Lenc8x_epilogue:
ret
.size aesni_multi_cbc_encrypt_avx,.-aesni_multi_cbc_encrypt_avx
.type aesni_multi_cbc_decrypt_avx,\@function,3
.align 32
aesni_multi_cbc_decrypt_avx:
_avx_cbc_dec_shortcut:
mov %rsp,%rax
push %rbx
push %rbp
push %r12
push %r13
push %r14
push %r15
___
$code.=<<___ if ($win64);
lea -0xa8(%rsp),%rsp
movaps %xmm6,(%rsp)
movaps %xmm7,0x10(%rsp)
movaps %xmm8,0x20(%rsp)
movaps %xmm9,0x30(%rsp)
movaps %xmm10,0x40(%rsp)
movaps %xmm11,0x50(%rsp)
movaps %xmm12,-0x78(%rax)
movaps %xmm13,-0x68(%rax)
movaps %xmm14,-0x58(%rax)
movaps %xmm15,-0x48(%rax)
___
$code.=<<___;
# stack layout
#
# +0 output sink
# +16 input sink [original %rsp and $num]
# +32 counters
# +64 distances between inputs and outputs
# +128 off-load area for @inp[0..3]
# +192 IV/input offload
sub \$256,%rsp
and \$-256,%rsp
sub \$192,%rsp
mov %rax,16(%rsp) # original %rsp
.Ldec8x_body:
vzeroupper
vmovdqu ($key),$zero # 0-round key
lea 0x78($key),$key # size optimization
lea 40*4($inp),$inp
shr \$1,$num
.Ldec8x_loop_grande:
#mov $num,24(%rsp) # original $num
xor $num,$num
___
for($i=0;$i<8;$i++) {
my $temp = $i ? $offload : $offset;
$code.=<<___;
mov `40*$i+16-40*4`($inp),$one # borrow $one for number of blocks
mov `40*$i+0-40*4`($inp),@ptr[$i] # input pointer
cmp $num,$one
mov `40*$i+8-40*4`($inp),$temp # output pointer
cmovg $one,$num # find maximum
test $one,$one
vmovdqu `40*$i+24-40*4`($inp),@out[$i] # load IV
mov $one,`32+4*$i`(%rsp) # initialize counters
cmovle %rsp,@ptr[$i] # cancel input
sub @ptr[$i],$temp # distance between input and output
mov $temp,`64+8*$i`(%rsp) # initialize distances
vmovdqu @out[$i],`192+16*$i`(%rsp) # offload IV
___
}
$code.=<<___;
test $num,$num
jz .Ldec8x_done
vmovups 0x10-0x78($key),$rndkey1
vmovups 0x20-0x78($key),$rndkey0
mov 0xf0-0x78($key),$rounds
lea 192+128(%rsp),$offload # offload area
vmovdqu (@ptr[0]),@out[0] # load inputs
vmovdqu (@ptr[1]),@out[1]
vmovdqu (@ptr[2]),@out[2]
vmovdqu (@ptr[3]),@out[3]
vmovdqu (@ptr[4]),@out[4]
vmovdqu (@ptr[5]),@out[5]
vmovdqu (@ptr[6]),@out[6]
vmovdqu (@ptr[7]),@out[7]
vmovdqu @out[0],0x00($offload) # offload inputs
vpxor $zero,@out[0],@out[0] # xor inputs with 0-round
vmovdqu @out[1],0x10($offload)
vpxor $zero,@out[1],@out[1]
vmovdqu @out[2],0x20($offload)
vpxor $zero,@out[2],@out[2]
vmovdqu @out[3],0x30($offload)
vpxor $zero,@out[3],@out[3]
vmovdqu @out[4],0x40($offload)
vpxor $zero,@out[4],@out[4]
vmovdqu @out[5],0x50($offload)
vpxor $zero,@out[5],@out[5]
vmovdqu @out[6],0x60($offload)
vpxor $zero,@out[6],@out[6]
vmovdqu @out[7],0x70($offload)
vpxor $zero,@out[7],@out[7]
xor \$0x80,$offload
mov \$1,$one # constant of 1
jmp .Loop_dec8x
.align 32
.Loop_dec8x:
___
for($i=0;$i<8;$i++) {
my $rndkey=($i&1)?$rndkey0:$rndkey1;
$code.=<<___;
vaesdec $rndkey,@out[0],@out[0]
cmp 32+4*$i(%rsp),$one
___
$code.=<<___ if ($i);
mov 64+8*$i(%rsp),$offset
___
$code.=<<___;
vaesdec $rndkey,@out[1],@out[1]
prefetcht0 31(@ptr[$i]) # prefetch input
vaesdec $rndkey,@out[2],@out[2]
___
$code.=<<___ if ($i>1);
prefetcht0 15(@ptr[$i-2]) # prefetch output
___
$code.=<<___;
vaesdec $rndkey,@out[3],@out[3]
lea (@ptr[$i],$offset),$offset
cmovge %rsp,@ptr[$i] # cancel input
vaesdec $rndkey,@out[4],@out[4]
cmovg %rsp,$offset # sink output
vaesdec $rndkey,@out[5],@out[5]
sub @ptr[$i],$offset
vaesdec $rndkey,@out[6],@out[6]
vmovdqu 16(@ptr[$i]),@inp[$i%4] # load input
mov $offset,64+8*$i(%rsp)
vaesdec $rndkey,@out[7],@out[7]
vmovups `16*(3+$i)-0x78`($key),$rndkey
lea 16(@ptr[$i],$offset),@ptr[$i] # switch to output
___
$code.=<<___ if ($i<4);
vmovdqu @inp[$i%4],`128+16*$i`(%rsp) # off-load
___
}
$code.=<<___;
vmovdqu 32(%rsp),$counters
prefetcht0 15(@ptr[$i-2]) # prefetch output
prefetcht0 15(@ptr[$i-1])
cmp \$11,$rounds
jb .Ldec8x_tail
vaesdec $rndkey1,@out[0],@out[0]
vaesdec $rndkey1,@out[1],@out[1]
vaesdec $rndkey1,@out[2],@out[2]
vaesdec $rndkey1,@out[3],@out[3]
vaesdec $rndkey1,@out[4],@out[4]
vaesdec $rndkey1,@out[5],@out[5]
vaesdec $rndkey1,@out[6],@out[6]
vaesdec $rndkey1,@out[7],@out[7]
vmovups 0xb0-0x78($key),$rndkey1
vaesdec $rndkey0,@out[0],@out[0]
vaesdec $rndkey0,@out[1],@out[1]
vaesdec $rndkey0,@out[2],@out[2]
vaesdec $rndkey0,@out[3],@out[3]
vaesdec $rndkey0,@out[4],@out[4]
vaesdec $rndkey0,@out[5],@out[5]
vaesdec $rndkey0,@out[6],@out[6]
vaesdec $rndkey0,@out[7],@out[7]
vmovups 0xc0-0x78($key),$rndkey0
je .Ldec8x_tail
vaesdec $rndkey1,@out[0],@out[0]
vaesdec $rndkey1,@out[1],@out[1]
vaesdec $rndkey1,@out[2],@out[2]
vaesdec $rndkey1,@out[3],@out[3]
vaesdec $rndkey1,@out[4],@out[4]
vaesdec $rndkey1,@out[5],@out[5]
vaesdec $rndkey1,@out[6],@out[6]
vaesdec $rndkey1,@out[7],@out[7]
vmovups 0xd0-0x78($key),$rndkey1
vaesdec $rndkey0,@out[0],@out[0]
vaesdec $rndkey0,@out[1],@out[1]
vaesdec $rndkey0,@out[2],@out[2]
vaesdec $rndkey0,@out[3],@out[3]
vaesdec $rndkey0,@out[4],@out[4]
vaesdec $rndkey0,@out[5],@out[5]
vaesdec $rndkey0,@out[6],@out[6]
vaesdec $rndkey0,@out[7],@out[7]
vmovups 0xe0-0x78($key),$rndkey0
.Ldec8x_tail:
vaesdec $rndkey1,@out[0],@out[0]
vpxor $zero,$zero,$zero
vaesdec $rndkey1,@out[1],@out[1]
vaesdec $rndkey1,@out[2],@out[2]
vpcmpgtd $zero,$counters,$zero
vaesdec $rndkey1,@out[3],@out[3]
vaesdec $rndkey1,@out[4],@out[4]
vpaddd $counters,$zero,$zero # decrement counters
vmovdqu 48(%rsp),$counters
vaesdec $rndkey1,@out[5],@out[5]
mov 64(%rsp),$offset # pre-load 1st offset
vaesdec $rndkey1,@out[6],@out[6]
vaesdec $rndkey1,@out[7],@out[7]
vmovups 0x10-0x78($key),$rndkey1
vaesdeclast $rndkey0,@out[0],@out[0]
vmovdqa $zero,32(%rsp) # update counters
vpxor $zero,$zero,$zero
vaesdeclast $rndkey0,@out[1],@out[1]
vpxor 0x00($offload),@out[0],@out[0] # xor with IV
vaesdeclast $rndkey0,@out[2],@out[2]
vpxor 0x10($offload),@out[1],@out[1]
vpcmpgtd $zero,$counters,$zero
vaesdeclast $rndkey0,@out[3],@out[3]
vpxor 0x20($offload),@out[2],@out[2]
vaesdeclast $rndkey0,@out[4],@out[4]
vpxor 0x30($offload),@out[3],@out[3]
vpaddd $zero,$counters,$counters # decrement counters
vmovdqu -0x78($key),$zero # 0-round
vaesdeclast $rndkey0,@out[5],@out[5]
vpxor 0x40($offload),@out[4],@out[4]
vaesdeclast $rndkey0,@out[6],@out[6]
vpxor 0x50($offload),@out[5],@out[5]
vmovdqa $counters,48(%rsp) # update counters
vaesdeclast $rndkey0,@out[7],@out[7]
vpxor 0x60($offload),@out[6],@out[6]
vmovups 0x20-0x78($key),$rndkey0
vmovups @out[0],-16(@ptr[0]) # write output
sub $offset,@ptr[0] # switch to input
vmovdqu 128+0(%rsp),@out[0]
vpxor 0x70($offload),@out[7],@out[7]
vmovups @out[1],-16(@ptr[1])
sub `64+1*8`(%rsp),@ptr[1]
vmovdqu @out[0],0x00($offload)
vpxor $zero,@out[0],@out[0]
vmovdqu 128+16(%rsp),@out[1]
vmovups @out[2],-16(@ptr[2])
sub `64+2*8`(%rsp),@ptr[2]
vmovdqu @out[1],0x10($offload)
vpxor $zero,@out[1],@out[1]
vmovdqu 128+32(%rsp),@out[2]
vmovups @out[3],-16(@ptr[3])
sub `64+3*8`(%rsp),@ptr[3]
vmovdqu @out[2],0x20($offload)
vpxor $zero,@out[2],@out[2]
vmovdqu 128+48(%rsp),@out[3]
vmovups @out[4],-16(@ptr[4])
sub `64+4*8`(%rsp),@ptr[4]
vmovdqu @out[3],0x30($offload)
vpxor $zero,@out[3],@out[3]
vmovdqu @inp[0],0x40($offload)
vpxor @inp[0],$zero,@out[4]
vmovups @out[5],-16(@ptr[5])
sub `64+5*8`(%rsp),@ptr[5]
vmovdqu @inp[1],0x50($offload)
vpxor @inp[1],$zero,@out[5]
vmovups @out[6],-16(@ptr[6])
sub `64+6*8`(%rsp),@ptr[6]
vmovdqu @inp[2],0x60($offload)
vpxor @inp[2],$zero,@out[6]
vmovups @out[7],-16(@ptr[7])
sub `64+7*8`(%rsp),@ptr[7]
vmovdqu @inp[3],0x70($offload)
vpxor @inp[3],$zero,@out[7]
xor \$128,$offload
dec $num
jnz .Loop_dec8x
mov 16(%rsp),%rax # original %rsp
#mov 24(%rsp),$num
#lea `40*8`($inp),$inp
#dec $num
#jnz .Ldec8x_loop_grande
.Ldec8x_done:
vzeroupper
___
$code.=<<___ if ($win64);
movaps -0xd8(%rax),%xmm6
movaps -0xc8(%rax),%xmm7
movaps -0xb8(%rax),%xmm8
movaps -0xa8(%rax),%xmm9
movaps -0x98(%rax),%xmm10
movaps -0x88(%rax),%xmm11
movaps -0x78(%rax),%xmm12
movaps -0x68(%rax),%xmm13
movaps -0x58(%rax),%xmm14
movaps -0x48(%rax),%xmm15
___
$code.=<<___;
mov -48(%rax),%r15
mov -40(%rax),%r14
mov -32(%rax),%r13
mov -24(%rax),%r12
mov -16(%rax),%rbp
mov -8(%rax),%rbx
lea (%rax),%rsp
.Ldec8x_epilogue:
ret
.size aesni_multi_cbc_decrypt_avx,.-aesni_multi_cbc_decrypt_avx
___
}}}
if ($win64) {
# EXCEPTION_DISPOSITION handler (EXCEPTION_RECORD *rec,ULONG64 frame,
# CONTEXT *context,DISPATCHER_CONTEXT *disp)
$rec="%rcx";
$frame="%rdx";
$context="%r8";
$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($context),%rbx # pull context->Rip
mov 8($disp),%rsi # disp->ImageBase
mov 56($disp),%r11 # disp->HandlerData
mov 0(%r11),%r10d # HandlerData[0]
lea (%rsi,%r10),%r10 # prologue label
cmp %r10,%rbx # context->Rip<.Lprologue
jb .Lin_prologue
mov 152($context),%rax # pull context->Rsp
mov 4(%r11),%r10d # HandlerData[1]
lea (%rsi,%r10),%r10 # epilogue label
cmp %r10,%rbx # context->Rip>=.Lepilogue
jae .Lin_prologue
mov 16(%rax),%rax # pull saved stack pointer
mov -8(%rax),%rbx
mov -16(%rax),%rbp
mov -24(%rax),%r12
mov -32(%rax),%r13
mov -40(%rax),%r14
mov -48(%rax),%r15
mov %rbx,144($context) # restore context->Rbx
mov %rbp,160($context) # restore context->Rbp
mov %r12,216($context) # restore cotnext->R12
mov %r13,224($context) # restore cotnext->R13
mov %r14,232($context) # restore cotnext->R14
mov %r15,240($context) # restore cotnext->R15
lea -56-10*16(%rax),%rsi
lea 512($context),%rdi # &context.Xmm6
mov \$20,%ecx
.long 0xa548f3fc # cld; rep movsq
.Lin_prologue:
mov 8(%rax),%rdi
mov 16(%rax),%rsi
mov %rax,152($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_aesni_multi_cbc_encrypt
.rva .LSEH_end_aesni_multi_cbc_encrypt
.rva .LSEH_info_aesni_multi_cbc_encrypt
.rva .LSEH_begin_aesni_multi_cbc_decrypt
.rva .LSEH_end_aesni_multi_cbc_decrypt
.rva .LSEH_info_aesni_multi_cbc_decrypt
___
$code.=<<___ if ($avx);
.rva .LSEH_begin_aesni_multi_cbc_encrypt_avx
.rva .LSEH_end_aesni_multi_cbc_encrypt_avx
.rva .LSEH_info_aesni_multi_cbc_encrypt_avx
.rva .LSEH_begin_aesni_multi_cbc_decrypt_avx
.rva .LSEH_end_aesni_multi_cbc_decrypt_avx
.rva .LSEH_info_aesni_multi_cbc_decrypt_avx
___
$code.=<<___;
.section .xdata
.align 8
.LSEH_info_aesni_multi_cbc_encrypt:
.byte 9,0,0,0
.rva se_handler
.rva .Lenc4x_body,.Lenc4x_epilogue # HandlerData[]
.LSEH_info_aesni_multi_cbc_decrypt:
.byte 9,0,0,0
.rva se_handler
.rva .Ldec4x_body,.Ldec4x_epilogue # HandlerData[]
___
$code.=<<___ if ($avx);
.LSEH_info_aesni_multi_cbc_encrypt_avx:
.byte 9,0,0,0
.rva se_handler
.rva .Lenc8x_body,.Lenc8x_epilogue # HandlerData[]
.LSEH_info_aesni_multi_cbc_decrypt_avx:
.byte 9,0,0,0
.rva se_handler
.rva .Ldec8x_body,.Ldec8x_epilogue # HandlerData[]
___
}
####################################################################
sub rex {
local *opcode=shift;
my ($dst,$src)=@_;
my $rex=0;
$rex|=0x04 if($dst>=8);
$rex|=0x01 if($src>=8);
push @opcode,$rex|0x40 if($rex);
}
sub aesni {
my $line=shift;
my @opcode=(0x66);
if ($line=~/(aeskeygenassist)\s+\$([x0-9a-f]+),\s*%xmm([0-9]+),\s*%xmm([0-9]+)/) {
rex(\@opcode,$4,$3);
push @opcode,0x0f,0x3a,0xdf;
push @opcode,0xc0|($3&7)|(($4&7)<<3); # ModR/M
my $c=$2;
push @opcode,$c=~/^0/?oct($c):$c;
return ".byte\t".join(',',@opcode);
}
elsif ($line=~/(aes[a-z]+)\s+%xmm([0-9]+),\s*%xmm([0-9]+)/) {
my %opcodelet = (
"aesimc" => 0xdb,
"aesenc" => 0xdc, "aesenclast" => 0xdd,
"aesdec" => 0xde, "aesdeclast" => 0xdf
);
return undef if (!defined($opcodelet{$1}));
rex(\@opcode,$3,$2);
push @opcode,0x0f,0x38,$opcodelet{$1};
push @opcode,0xc0|($2&7)|(($3&7)<<3); # ModR/M
return ".byte\t".join(',',@opcode);
}
elsif ($line=~/(aes[a-z]+)\s+([0x1-9a-fA-F]*)\(%rsp\),\s*%xmm([0-9]+)/) {
my %opcodelet = (
"aesenc" => 0xdc, "aesenclast" => 0xdd,
"aesdec" => 0xde, "aesdeclast" => 0xdf
);
return undef if (!defined($opcodelet{$1}));
my $off = $2;
push @opcode,0x44 if ($3>=8);
push @opcode,0x0f,0x38,$opcodelet{$1};
push @opcode,0x44|(($3&7)<<3),0x24; # ModR/M
push @opcode,($off=~/^0/?oct($off):$off)&0xff;
return ".byte\t".join(',',@opcode);
}
return $line;
}
$code =~ s/\`([^\`]*)\`/eval($1)/gem;
$code =~ s/\b(aes.*%xmm[0-9]+).*$/aesni($1)/gem;
print $code;
close STDOUT;
| dkoontz/nodegit | vendor/openssl/openssl/crypto/aes/asm/aesni-mb-x86_64.pl | Perl | mit | 35,969 |
package DDG::Goodie::SumOfNaturalNumbers;
# ABSTRACT: Returns the sum of the numbers between the first and second provided integers
use strict;
use DDG::Goodie;
use bignum;
triggers start => "add", "sum from";
triggers startend => "sum";
zci is_cached => 1;
zci answer_type => "sum";
primary_example_queries 'sum 1 to 10';
secondary_example_queries 'add 33 to 100';
description 'Add up the numbers between two values';
name 'SumOfNaturalNumbers';
code_url 'https://github.com/duckduckgo/zeroclickinfo-goodies/blob/master/lib/DDG/Goodie/SumOfNaturalNumbers.pm';
category 'calculations';
topics 'math';
attribution github => ['JulianGindi', 'Julian Gindi'],
github => ['navneet35371', 'Navneet Suman'];
# This adds commas to the number.
# It converts 10000000 to 10,000,000.
# It was copied from http://perldoc.perl.org/perlfaq5.html#How-can-I-output-my-numbers-with-commas-added%3f
sub commify {
# Disable bigint in this function. It interferes with `1 while ...`.
no bigint;
local $_ = shift;
1 while s/^([-+]?\d+)(\d{3})/$1,$2/;
return $_;
}
handle remainder => sub {
# Check if we're getting integers.
return unless $_ =~ /^(?:from )?(\d+)\s*(to|-)\s*(\d+)$/i;
if ($1 > $3) {
return;
} else {
my $sum = ((($3 * ($3 + 1)) / 2)-(($1 * ($1 - 1)) / 2));
return 'Sum of natural numbers from ' . commify($1) . ' to ' . commify($3) . ' is ' . commify($sum) . '.';
}
};
1;
| sagarhani/zeroclickinfo-goodies | lib/DDG/Goodie/SumOfNaturalNumbers.pm | Perl | apache-2.0 | 1,431 |
=head1 NAME
CXGN::List::Transform - transform lists from one type to another
=head1 SYNOPSYS
my $tf = CXGN::List::Transform->new();
if (my $transform_name = $tf->can_transform("accessions", "accession_ids")) {
my $tf_list = @$tf->tranform($schema, $transform_name, $list_ref);
}
=cut
package CXGN::List::Transform;
use Moose;
use Data::Dumper;
use Module::Pluggable require => 1;
=head2 can_transform
Usage: my $tf_name = $tf->can_transform("accessions", "accession_ids");
Desc: ask if to types can be transformed. Returns the name of the
transform, to be used with the transform() function
Ret:
Args:
Side Effects:
Example:
=cut
sub can_transform {
my $self = shift;
my $type1 = shift;
my $type2 = shift;
foreach my $p ($self->plugins()) {
if ($p->can_transform($type1, $type2)) {
return $p->name();
}
}
return 0;
}
=head2 transform
Usage: $tf->transform($schema, $transform_name, $list_ref);
Desc:
Args: $schema (Bio::Chado::Schema)
$transform_name (obtain from can_transform())
$list_ref of elements to transform
Returns: a hashref with two keys, transform and missing, both
of which are arrayrefs of strings.
Side Effects:
Example:
=cut
sub transform {
my $self = shift;
my $schema = shift;
my $transform_name = shift;
my $list = shift;
my $data;
foreach my $p ($self->plugins()) {
if ($transform_name eq $p->name()) {
$data = $p->transform($schema, $list, $self);
}
}
return $data;
}
1;
| solgenomics/sgn | lib/CXGN/List/Transform.pm | Perl | mit | 1,616 |
package XML::Grammar::Fiction::App::ToDocBook;
use strict;
use warnings;
use autodie;
use base 'Exporter';
our @EXPORT = (qw(run));
use Getopt::Long;
use XML::Grammar::Fiction::ToDocBook;
our $VERSION = '0.14.11';
sub run
{
my $output_filename;
GetOptions(
"output|o=s" => \$output_filename,
);
if (!defined($output_filename))
{
die "Output filename not specified! Use the -o|--output flag!";
}
my $converter = XML::Grammar::Fiction::ToDocBook->new();
my $output_text = $converter->translate_to_docbook({
source => { file => shift(@ARGV), },
output => "string",
}
);
open my $out, ">", $output_filename;
binmode $out, ":utf8";
print {$out} $output_text;
close($out);
exit(0);
}
1;
__END__
=pod
=encoding UTF-8
=head1 NAME
XML::Grammar::Fiction::App::ToDocBook - command line app-in-a-module
to convert a Fiction XML file to DocBook 5.
=head1 VERSION
version 0.14.11
=head1 SYNOPSIS
perl -MXML::Grammar::Fiction::App::ToDocBook -e 'run()' -- \
-o "$OUTPUT_FILE" "$INPUT_FILE"
=head1 VERSION
Version 0.14.11
=head1 FUNCTIONS
=head2 run()
Call with no arguments to run the application from the commandline.
=head1 AUTHOR
Shlomi Fish <shlomif@cpan.org>
=head1 COPYRIGHT AND LICENSE
This software is Copyright (c) 2007 by Shlomi Fish.
This is free software, licensed under:
The MIT (X11) License
=head1 BUGS
Please report any bugs or feature requests on the bugtracker website
http://rt.cpan.org/NoAuth/Bugs.html?Dist=XML-Grammar-Fiction or by email to
bug-xml-grammar-fiction@rt.cpan.org.
When submitting a bug or request, please include a test-file or a
patch to an existing test-file that illustrates the bug or desired
feature.
=for :stopwords cpan testmatrix url annocpan anno bugtracker rt cpants kwalitee diff irc mailto metadata placeholders metacpan
=head1 SUPPORT
=head2 Perldoc
You can find documentation for this module with the perldoc command.
perldoc XML::Grammar::Fiction
=head2 Websites
The following websites have more information about this module, and may be of help to you. As always,
in addition to those websites please use your favorite search engine to discover more resources.
=over 4
=item *
MetaCPAN
A modern, open-source CPAN search engine, useful to view POD in HTML format.
L<http://metacpan.org/release/XML-Grammar-Fiction>
=item *
Search CPAN
The default CPAN search engine, useful to view POD in HTML format.
L<http://search.cpan.org/dist/XML-Grammar-Fiction>
=item *
RT: CPAN's Bug Tracker
The RT ( Request Tracker ) website is the default bug/issue tracking system for CPAN.
L<http://rt.cpan.org/NoAuth/Bugs.html?Dist=XML-Grammar-Fiction>
=item *
AnnoCPAN
The AnnoCPAN is a website that allows community annotations of Perl module documentation.
L<http://annocpan.org/dist/XML-Grammar-Fiction>
=item *
CPAN Ratings
The CPAN Ratings is a website that allows community ratings and reviews of Perl modules.
L<http://cpanratings.perl.org/d/XML-Grammar-Fiction>
=item *
CPAN Forum
The CPAN Forum is a web forum for discussing Perl modules.
L<http://cpanforum.com/dist/XML-Grammar-Fiction>
=item *
CPANTS
The CPANTS is a website that analyzes the Kwalitee ( code metrics ) of a distribution.
L<http://cpants.perl.org/dist/overview/XML-Grammar-Fiction>
=item *
CPAN Testers
The CPAN Testers is a network of smokers who run automated tests on uploaded CPAN distributions.
L<http://www.cpantesters.org/distro/X/XML-Grammar-Fiction>
=item *
CPAN Testers Matrix
The CPAN Testers Matrix is a website that provides a visual overview of the test results for a distribution on various Perls/platforms.
L<http://matrix.cpantesters.org/?dist=XML-Grammar-Fiction>
=item *
CPAN Testers Dependencies
The CPAN Testers Dependencies is a website that shows a chart of the test results of all dependencies for a distribution.
L<http://deps.cpantesters.org/?module=XML::Grammar::Fiction>
=back
=head2 Bugs / Feature Requests
Please report any bugs or feature requests by email to C<bug-xml-grammar-fiction at rt.cpan.org>, or through
the web interface at L<http://rt.cpan.org/NoAuth/ReportBug.html?Queue=XML-Grammar-Fiction>. You will be automatically notified of any
progress on the request by the system.
=head2 Source Code
The code is open to the world, and available for you to hack on. Please feel free to browse it and play
with it, or whatever. If you want to contribute patches, please send me a diff or prod me to pull
from your repository :)
L<http://bitbucket.org/shlomif/perl-XML-Grammar-Fiction>
hg clone ssh://hg@bitbucket.org/shlomif/perl-XML-Grammar-Fiction
=cut
| gitpan/XML-Grammar-Fiction | lib/XML/Grammar/Fiction/App/ToDocBook.pm | Perl | mit | 4,695 |
=head1 NAME
Mail::Message::Convert::MailInternet - translate Mail::Message to Mail::Internet vv
=head1 INHERITANCE
Mail::Message::Convert::MailInternet
is a Mail::Message::Convert
is a Mail::Reporter
=head1 SYNOPSIS
use Mail::Message::Convert::MailInternet;
my $convert = Mail::Message::Convert::MailInternet->new;
my Mail::Message $msg = Mail::Message->new;
my Mail::Internet $intern = $convert->export($msg);
my Mail::Internet $intern = Mail::Internet->new;
my Mail::Message $msg = $convert->from($intern);
use Mail::Box::Manager;
my $mgr = Mail::Box::Manager->new;
my $folder = $mgr->open(folder => 'Outbox');
$folder->addMessage($intern);
=head1 DESCRIPTION
The L<Mail::Internet|Mail::Internet> class of messages is very popular for all
kinds of message applications written in Perl. However, the
format was developed when e-mail messages where still small and
attachments where rare; Mail::Message is much more flexible in
this respect.
=head2 Converters between message objects
=head2 Other converters
=head1 METHODS
=head2 Constructors
Mail::Message::Convert::MailInternet-E<gt>B<new>(OPTIONS)
=over 4
See L<Mail::Message::Convert/"METHODS">
=back
=head2 Converting
$obj-E<gt>B<export>(MESSAGE, OPTIONS)
=over 4
Returns a new message object based on the information from
a L<Mail::Message|Mail::Message> object. The MESSAGE specified is an
instance of a Mail::Message.
example:
my $convert = Mail::Message::Convert::MailInternet->new;
my Mail::Message $msg = Mail::Message->new;
my Mail::Internet $copy = $convert->export($msg);
=back
$obj-E<gt>B<from>(OBJECT, OPTIONS)
=over 4
Returns a new L<Mail::Message|Mail::Message> object based on the information
from a L<Mail::Internet|Mail::Internet> object.
example:
my $convert = Mail::Message::Convert::MailInternet->new;
my Mail::Internet $msg = Mail::Internet->new;
my Mail::Message $copy = $convert->from($msg);
=back
$obj-E<gt>B<selectedFields>(HEAD)
=over 4
See L<Mail::Message::Convert/"Converting">
=back
=head2 Error handling
$obj-E<gt>B<AUTOLOAD>
=over 4
See L<Mail::Reporter/"Error handling">
=back
$obj-E<gt>B<addReport>(OBJECT)
=over 4
See L<Mail::Reporter/"Error handling">
=back
$obj-E<gt>B<defaultTrace>([LEVEL]|[LOGLEVEL, TRACELEVEL]|[LEVEL, CALLBACK])
Mail::Message::Convert::MailInternet-E<gt>B<defaultTrace>([LEVEL]|[LOGLEVEL, TRACELEVEL]|[LEVEL, CALLBACK])
=over 4
See L<Mail::Reporter/"Error handling">
=back
$obj-E<gt>B<errors>
=over 4
See L<Mail::Reporter/"Error handling">
=back
$obj-E<gt>B<log>([LEVEL [,STRINGS]])
Mail::Message::Convert::MailInternet-E<gt>B<log>([LEVEL [,STRINGS]])
=over 4
See L<Mail::Reporter/"Error handling">
=back
$obj-E<gt>B<logPriority>(LEVEL)
Mail::Message::Convert::MailInternet-E<gt>B<logPriority>(LEVEL)
=over 4
See L<Mail::Reporter/"Error handling">
=back
$obj-E<gt>B<logSettings>
=over 4
See L<Mail::Reporter/"Error handling">
=back
$obj-E<gt>B<notImplemented>
=over 4
See L<Mail::Reporter/"Error handling">
=back
$obj-E<gt>B<report>([LEVEL])
=over 4
See L<Mail::Reporter/"Error handling">
=back
$obj-E<gt>B<reportAll>([LEVEL])
=over 4
See L<Mail::Reporter/"Error handling">
=back
$obj-E<gt>B<trace>([LEVEL])
=over 4
See L<Mail::Reporter/"Error handling">
=back
$obj-E<gt>B<warnings>
=over 4
See L<Mail::Reporter/"Error handling">
=back
=head2 Cleanup
$obj-E<gt>B<DESTROY>
=over 4
See L<Mail::Reporter/"Cleanup">
=back
$obj-E<gt>B<inGlobalDestruction>
=over 4
See L<Mail::Reporter/"Cleanup">
=back
=head1 DIAGNOSTICS
Error: Package $package does not implement $method.
=over 4
Fatal error: the specific package (or one of its superclasses) does not
implement this method where it should. This message means that some other
related classes do implement this method however the class at hand does
not. Probably you should investigate this and probably inform the author
of the package.
=back
=head1 SEE ALSO
This module is part of Mail-Box distribution version 2.082,
built on April 28, 2008. Website: F<http://perl.overmeer.net/mailbox/>
=head1 LICENSE
Copyrights 2001-2008 by Mark Overmeer. For other contributors see ChangeLog.
This program is free software; you can redistribute it and/or modify it
under the same terms as Perl itself.
See F<http://www.perl.com/perl/misc/Artistic.html>
| carlgao/lenga | images/lenny64-peon/usr/share/perl5/Mail/Message/Convert/MailInternet.pod | Perl | mit | 4,354 |
##############################################################################
# $URL: http://perlcritic.tigris.org/svn/perlcritic/trunk/distributions/Perl-Critic/lib/Perl/Critic/Policy/CodeLayout/ProhibitQuotedWordLists.pm $
# $Date: 2012-07-02 22:16:39 -0700 (Mon, 02 Jul 2012) $
# $Author: thaljef $
# $Revision: 4126 $
##############################################################################
package Perl::Critic::Policy::CodeLayout::ProhibitQuotedWordLists;
use 5.006001;
use strict;
use warnings;
use Readonly;
use Perl::Critic::Utils qw{ :characters :severities :classification};
use base 'Perl::Critic::Policy';
our $VERSION = '1.118';
#-----------------------------------------------------------------------------
Readonly::Scalar my $DESC => q{List of quoted literal words};
Readonly::Scalar my $EXPL => q{Use 'qw()' instead};
#-----------------------------------------------------------------------------
sub supported_parameters {
return (
{
name => 'min_elements',
description => 'The minimum number of words in a list that will be complained about.',
default_string => '2',
behavior => 'integer',
integer_minimum => 1,
},
{
name => 'strict',
description => 'Complain even if there are non-word characters in the values.',
default_string => '0',
behavior => 'boolean',
},
);
}
sub default_severity { return $SEVERITY_LOW }
sub default_themes { return qw( core cosmetic ) }
sub applies_to { return 'PPI::Structure::List' }
#-----------------------------------------------------------------------------
sub violates {
my ( $self, $elem, undef ) = @_;
# Don't worry about subroutine calls
my $sibling = $elem->sprevious_sibling();
return if not $sibling;
return if $sibling->isa('PPI::Token::Symbol');
return if $sibling->isa('PPI::Token::Operator') and $sibling eq '->';
return if $sibling->isa('PPI::Token::Word') and not is_included_module_name($sibling);
# Get the list elements
my $expr = $elem->schild(0);
return if not $expr;
my @children = $expr->schildren();
return if not @children;
my $count = 0;
for my $child ( @children ) {
next if $child->isa('PPI::Token::Operator') && $child eq $COMMA;
# All elements must be literal strings,
# and must contain 1 or more word characters.
return if not _is_literal($child);
my $string = $child->string();
return if $string =~ m{ \s }xms;
return if $string eq $EMPTY;
return if not $self->{_strict} and $string !~ m{\A [\w-]+ \z}xms;
$count++;
}
# Were there enough?
return if $count < $self->{_min_elements};
# If we get here, then all elements were literals
return $self->violation( $DESC, $EXPL, $elem );
}
sub _is_literal {
my $elem = shift;
return $elem->isa('PPI::Token::Quote::Single')
|| $elem->isa('PPI::Token::Quote::Literal');
}
1;
__END__
=pod
=head1 NAME
Perl::Critic::Policy::CodeLayout::ProhibitQuotedWordLists - Write C<qw(foo bar baz)> instead of C<('foo', 'bar', 'baz')>.
=head1 AFFILIATION
This Policy is part of the core L<Perl::Critic|Perl::Critic>
distribution.
=head1 DESCRIPTION
Conway doesn't mention this, but I think C<qw()> is an underused
feature of Perl. Whenever you need to declare a list of one-word
literals, the C<qw()> operator is wonderfully concise, and makes it
easy to add to the list in the future.
@list = ('foo', 'bar', 'baz'); #not ok
@list = qw(foo bar baz); #ok
use Foo ('foo', 'bar', 'baz'); #not ok
use Foo qw(foo bar baz); #ok
=head1 CONFIGURATION
This policy can be configured to only pay attention to word lists with
at least a particular number of elements. By default, this value is
2, which means that lists containing zero or one elements are ignored.
The minimum list size to be looked at can be specified by giving a
value for C<min_elements> in F<.perlcriticrc> like this:
[CodeLayout::ProhibitQuotedWordLists]
min_elements = 4
This would cause this policy to only complain about lists containing
four or more words.
By default, this policy won't complain if any of the values in the list
contain non-word characters. If you want it to, set the C<strict>
option to a true value.
[CodeLayout::ProhibitQuotedWordLists]
strict = 1
=head1 NOTES
In the PPI parlance, a "list" is almost anything with parentheses.
I've tried to make this Policy smart by targeting only "lists" that
could be sensibly expressed with C<qw()>. However, there may be some
edge cases that I haven't covered. If you find one, send me a note.
=head1 IMPORTANT CHANGES
This policy was formerly called C<RequireQuotedWords> which seemed a
little counter-intuitive. If you get lots of "Cannot load policy
module" errors, then you probably need to change C<RequireQuotedWords>
to C<ProhibitQuotedWordLists> in your F<.perlcriticrc> file.
=head1 AUTHOR
Jeffrey Ryan Thalhammer <jeff@imaginative-software.com>
=head1 COPYRIGHT
Copyright (c) 2005-2011 Imaginative Software Systems. All rights reserved.
This program is free software; you can redistribute it and/or modify
it under the same terms as Perl itself. The full text of this license
can be found in the LICENSE file included with this module.
=cut
# Local Variables:
# mode: cperl
# cperl-indent-level: 4
# fill-column: 78
# indent-tabs-mode: nil
# c-indentation-style: bsd
# End:
# ex: set ts=8 sts=4 sw=4 tw=78 ft=perl expandtab shiftround :
| amidoimidazol/bio_info | Beginning Perl for Bioinformatics/lib/Perl/Critic/Policy/CodeLayout/ProhibitQuotedWordLists.pm | Perl | mit | 5,701 |
package FIG_Config;
## WHEN YOU ADD ITEMS TO THIS FILE, BE SURE TO UPDATE kernel/scripts/Config.pl.
## All paths should be absolute, not relative.
# root directory of the local web server
our $web_dir = "";
# TRUE for windows mode
our $win_mode = 0;
# source code project directory
our $proj = "/kb/module/SEEDtk";
# location of shared code
our $cvsroot = "";
# TRUE to switch to the data directory during setup
our $data_switch = 0;
# location of global file directory
our $global = "/kb/module/SEEDtk/Data/Global";
# default conserved domain search URL
our $ConservedDomainSearchURL = "http://maple.mcs.anl.gov:5600";
# Patric Data API URL
our $p3_data_api_url = "";
# code module base directory
our $mod_base = '/kb/module/SEEDtk/modules';
# list of script directories
our @scripts = ('/kb/module/SEEDtk/modules/tbltools/scripts', '/kb/module/SEEDtk/modules/RASTtk/scripts', '/kb/module/SEEDtk/modules/kernel/scripts', '/kb/module/SEEDtk/modules/ERDB/scripts', '/kb/module/SEEDtk/modules/utils/scripts');
# list of PERL libraries
our @libs = ('/kb/module/SEEDtk/config', '/kb/module/SEEDtk/modules/tbltools/lib', '/kb/module/SEEDtk/modules/RASTtk/lib', '/kb/module/SEEDtk/modules/kernel/lib', '/kb/module/SEEDtk/modules/ERDB/lib', '/kb/module/SEEDtk/modules/utils/lib');
# list of project modules
our @modules = qw(tbltools RASTtk kernel ERDB utils);
# list of shared modules
our @shared = qw();
# list of tool directories
our @tools = ();
# SHRUB CONFIGURATION
# root directory for Shrub data files (should have
# subdirectories "Inputs" (optional) and "LoadFiles"
# (required))
our $data = "/kb/module/SEEDtk/Data";
# full name of the Shrub DBD XML file
our $shrub_dbd = "/kb/module/SEEDtk/modules/ERDB/ShrubDBD.xml";
# Shrub database signon info (name/password)
our $userData = "seedtk/when26crazy";
# name of the Shrub database (empty string to use the
# default)
our $shrubDB = "seedtk_shrub";
# TRUE if we should create indexes before a table load
# (generally TRUE for MySQL, FALSE for PostGres)
our $preIndex = 1;
# default DBMS (currently only "mysql" works for sure)
our $dbms = "mysql";
# database access port
our $dbport = 3306;
# TRUE if we are using an old version of MySQL (legacy
# parameter; may go away)
our $mysql_v3 = 0;
# default MySQL storage engine
our $default_mysql_engine = "InnoDB";
# database host server (empty string to use the default)
our $dbhost = "db3.chicago.kbase.us";
#our $dbhost = "branch.mcs.anl.gov";
# TRUE to turn off size estimates during table creation--
# should be FALSE for MyISAM
our $disable_dbkernel_size_estimates = 1;
# mode for LOAD TABLE INFILE statements, empty string is OK
# except in special cases (legacy parameter; may go away)
our $load_mode = "";
# location of the DNA repository
our $shrub_dna = "";
# Insure the PATH has our scripts in it.
$_ = "/homes/janakae/KServices/atomic_regulons/SEEDtk/bin";
if (! $ENV{PATH}) {
$ENV{PATH} = $_;
} elsif (substr($ENV{PATH}, 0, 51) ne $_) {
$ENV{PATH} = "$_:$ENV{PATH}";
}
# Insure the PERL5LIB has our libraries in it.
$_ = "/kb/module/SEEDtk/modules/tbltools/lib:/kb/module/SEEDtk/modules/RASTtk/lib:/kb/module/SEEDtk/modules/kernel/lib:/kb/module/SEEDtk/modules/ERDB/lib:/kb/module/SEEDtk/modules/utils/lib:/homes/janakae/KServices/atomic_regulons/SEEDtk/config";
if (! $ENV{PERL5LIB}) {
$ENV{PERL5LIB} = $_;
} elsif (substr($ENV{PERL5LIB}, 0, 238) ne $_) {
$ENV{PERL5LIB} = "$_:$ENV{PERL5LIB}";
}
# Add include paths.
push @INC, '/kb/module/SEEDtk/modules/tbltools/lib', '/kb/module/SEEDtk/modules/RASTtk/lib', '/kb/module/SEEDtk/modules/kernel/lib', '/kb/module/SEEDtk/modules/ERDB/lib', '/kb/module/SEEDtk/modules/utils/lib';
1;
| janakagithub/atomic_regulons | lib/FIG_Config.pm | Perl | mit | 4,019 |
name(pcache).
version('0.1.0').
requires(rocksdb).
requires(prolog >= '7.5.14').
title('Persistent answer cache').
keywords([cache, memoize, persistency]).
author( 'Jan Wielemaker', 'jan@swi-prolog.org' ).
home('https://github.com/JanWielemaker/pcache' ).
download('https://github.com/JanWielemaker/pcache/releases/*.zip').
| TeamSPoon/logicmoo_workspace | packs_web/swish/pack/pcache/pack.pl | Perl | mit | 324 |
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fr(202165616,1,0).
fr(202165616,6,0).
fr(202165758,1,0).
fr(202165758,2,0).
fr(202165898,22,0).
fr(202166027,4,0).
fr(202166195,22,0).
fr(202166357,4,0).
fr(202166479,1,0).
fr(202166479,4,0).
fr(202166619,4,0).
fr(202166820,8,0).
fr(202167002,4,0).
fr(202167117,9,0).
fr(202167274,6,0).
fr(202167415,11,0).
fr(202167557,11,0).
fr(202167692,4,0).
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fr(202168016,11,0).
fr(202168151,22,0).
fr(202168274,11,0).
fr(202168409,11,0).
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fr(202168736,1,0).
fr(202168854,11,0).
fr(202169241,11,0).
fr(202169338,1,0).
fr(202169338,4,0).
fr(202169608,1,0).
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fr(202169785,8,0).
fr(202169785,11,0).
fr(202169962,11,0).
fr(202170093,1,0).
fr(202170233,1,0).
fr(202170347,9,0).
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fr(202170461,4,0).
fr(202170593,11,0).
fr(202170787,11,0).
fr(202170927,11,0).
fr(202171024,11,0).
fr(202171119,11,0).
fr(202171254,11,0).
fr(202171372,1,0).
fr(202171372,2,0).
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fr(202171372,22,0).
fr(202171622,22,0).
fr(202171900,1,0).
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fr(202172226,22,0).
fr(202172427,1,0).
fr(202172427,11,0).
fr(202172619,6,0).
fr(202172799,1,0).
fr(202172945,1,0).
fr(202173081,1,0).
fr(202173245,1,0).
fr(202173382,8,0).
fr(202173534,1,0).
fr(202173652,1,0).
fr(202173797,1,0).
fr(202173871,11,0).
fr(202174053,1,0).
fr(202174204,4,0).
fr(202174359,1,0).
fr(202174512,1,0).
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fr(202174897,3,0).
fr(202174897,11,0).
fr(202175124,1,0).
fr(202175124,8,0).
fr(202175449,1,0).
fr(202175571,1,0).
fr(202175706,3,0).
fr(202175846,3,0).
fr(202175987,3,0).
fr(202176156,3,0).
fr(202176367,3,0).
fr(202176504,1,0).
fr(202176504,4,0).
fr(202176668,1,0).
fr(202176668,3,0).
fr(202176913,3,0).
fr(202177028,3,0).
fr(202177130,3,0).
fr(202177251,3,0).
fr(202177422,1,0).
fr(202177557,8,0).
fr(202177557,11,0).
fr(202177884,8,0).
fr(202177884,11,0).
fr(202178089,8,0).
fr(202178240,8,0).
fr(202178367,1,0).
fr(202178649,1,0).
fr(202178744,1,0).
fr(202178887,8,0).
fr(202178887,11,0).
fr(202179091,8,0).
fr(202179182,1,0).
fr(202179340,8,0).
fr(202179340,11,0).
fr(202179604,8,0).
fr(202179604,11,0).
fr(202179784,11,0).
fr(202179918,8,0).
fr(202179918,11,0).
fr(202180166,1,0).
fr(202180323,1,0).
fr(202180490,11,0).
fr(202180607,8,0).
fr(202180607,21,0).
fr(202180762,1,0).
fr(202180903,1,0).
fr(202181016,1,0).
fr(202181380,1,0).
fr(202181503,1,0).
fr(202181614,1,0).
fr(202181772,1,0).
fr(202181905,1,0).
fr(202182131,1,0).
fr(202182286,1,0).
fr(202182427,1,0).
fr(202182624,8,0).
fr(202182624,11,0).
fr(202182780,11,0).
fr(202182935,1,0).
fr(202183180,1,0).
fr(202183293,1,0).
fr(202183446,1,0).
fr(202183612,10,0).
fr(202183612,11,0).
fr(202183767,1,0).
fr(202183767,11,0).
fr(202183887,8,0).
fr(202183887,11,0).
fr(202184303,11,0).
fr(202184447,1,0).
fr(202184527,1,0).
fr(202184666,11,0).
fr(202184838,11,0).
fr(202184968,1,0).
fr(202184968,2,0).
fr(202185091,9,0).
fr(202185091,10,0).
fr(202185091,11,0).
fr(202185209,1,0).
fr(202185394,1,0).
fr(202185558,1,0).
fr(202185558,3,0).
fr(202185558,4,0).
fr(202185779,1,0).
fr(202185779,3,0).
fr(202185779,4,0).
fr(202185923,1,0).
fr(202186064,1,0).
fr(202186064,4,0).
fr(202186181,3,0).
fr(202186282,1,0).
fr(202186415,3,0).
fr(202186589,3,0).
fr(202186744,3,0).
fr(202186908,11,0).
fr(202187121,1,0).
fr(202187121,3,0).
fr(202187270,1,0).
fr(202187270,3,0).
fr(202187421,10,0).
fr(202187421,11,0).
fr(202187575,1,0).
fr(202187575,11,0).
fr(202187749,1,0).
fr(202187881,1,0).
fr(202187881,3,0).
fr(202187990,8,0).
| TeamSPoon/logicmoo_workspace | packs_sys/logicmoo_nlu/data/WNprolog-1.7.1/prolog/wn_fr.pl | Perl | mit | 406,003 |
#!/usr/env/perl
# (C) 2016 http://www.enviroware.com
# Version 20160526
# Type perl wps_help.pl -info=VARIABLE to get help on WPS VARAIBLE (WRF 3.8).
# Type perl wps_help.pl --help to get a list of variables
use strict;
use Data::Dumper;
use Getopt::Long;
my %manual;
load_manual();
my %input;
my @input_list;
my $show_help_info = '';
init_input();
GetOptions(@input_list,'help'=>\$show_help_info);
print_info();
#ADD---------------------------------------------------------------------
#---------------------------------------------------------------------
sub init_input {
%input = (
info => '',
# SHARE section
wrf_core => 'ARW',
max_dom => 1,
start_year => '',
start_month => '',
start_day => '',
start_hour => '',
end_year => '',
end_month => '',
end_day => '',
end_hour => '',
start_date => '',
end_date => '',
interval_seconds => '',
active_grid => 'T',
io_form_geogrid => 2,
opt_output_from_geogrid_path => './',
debug_level => 0,
# GEOGRID section
parent_id => 1,
parent_grid_ratio => '',
i_parent_start => '',
j_parent_start => '',
s_we => 1,
e_we => '',
s_sn => 1,
e_sn => '',
geog_data_res => 'default',
dx => '',
dy => '',
map_proj => 'lambert',
ref_lat => -999,
ref_lon => -999,
ref_x => '',
ref_y => '',
truelat1 => '',
truelat2 => '',
stand_lon => '',
pole_lat => '',
pole_lon => '',
geog_data_path => '',
opt_geogrid_tbl_path => './geogrid/',
# UNGRIB section
out_format => 'WPS',
prefix => 'FILE',
# METGRID section
fg_name => '',
constants_name => '',
io_form_metgrid => 2,
opt_output_from_metgrid_path => './',
opt_metgrid_tbl_path => './metgrid/',
process_only_bdy => 0,
#
);
my @numerics = qw(
max_dom
start_year start_month start_day start_hour
end_year end_month end_day end_hour
interval_seconds io_form_geogrid
debug_level
parent_id parent_grid_ratio i_parent_start j_parent_start
s_we e_we s_sn e_sn
ref_lon ref_lat dx dy ref_x ref_y truelat1 truelat2 stang_lon pole_lat pole_lon
io_form_metgrid process_only_bdy
);
map {
push @input_list, "$_=i" => \$input{$_};
} (@numerics);
my @flags = qw(
info wrf_core opt_output_from_geogrid_path geogrid map_proj geog_data_path
opt_geogrid_tbl_path start_date end_date out_format prefix fg_name constants_name
opt_output_from_geogrid_path opt_metgrid_tbl_path
);
map {
push @input_list, "$_=s" => \$input{$_};
} (@flags);
}
# ---------------------------------------------------------------------------- #
sub print_info {
if ($show_help_info) {
print "\nType perl wps_manager.pl -info=VARIABLE to get help.\n
The help is available for
** SHARE section:
This section describes variables that are used by more than one WPS program.
For example, the wrf_core variable specifies whether the WPS is to produce data
for the ARW or the NMM core – information which is needed by both the geogrid
and metgrid programs.
VARIABLES: wrf_core, max_dom, start_year, start_month, start_day, start_hour,
end_year, end_month, end_day, end_hour, start_date, end_date,
interval_seconds, active_grid, io_form_geogrid,
opt_output_from_geogrid_path, debug_level
** GEOGRID section:
This section specifies variables that are specific to the geogrid program.
Variables in the geogrid section primarily define the size and location
of all model domains, and where the static geographical data are found.
VARIABLES: parent_id, parent_grid_ratio, i_parent_start, j_parent_start,
s_we, e_we, s_sn, e_sn, geog_data_res, dx, dy, map_proj,
ref_lat, ref_lon, ref_x, ref_y, truelat1, truelat2, stand_lon,
pole_lat, pole_lon, geog_data_path, opt_geogrid_tbl_path
** UNGRIB section:
out_format, prefix
** METGRID section:
fg_name, constants_name, io_form_metgrid,
opt_output_from_metgrid_path, opt_metgrid_tbl_path,
process_only_bdy
";
exit;
}
return unless ($input{info});
my $item = uc($input{info}) || '';
return unless ($item);
my $content = $manual{$item} || '';
print "** $item **\n";
if ($content) {
print $manual{$item},"\n";
} else {
print "No manual entry.\n";
}
exit;
}
# ---------------------------------------------------------------------------- #
sub load_manual {
# from http://www2.mmm.ucar.edu/wrf/users/docs/user_guide_V3.8/users_guide_chap3.htm#_Description_of_the_1
%manual = (
# SHARE section
WRF_CORE => qq(A character string set to either 'ARW' or 'NMM' that tells the WPS which dynamical core the input data are being prepared for. Default value is 'ARW'.),
MAX_DOM => qq(An integer specifying the total number of domains/nests, including the parent domain, in the simulation. Default value is 1.),
START_YEAR => qq(A list of MAX_DOM 4-digit integers specifying the starting UTC year of the simulation for each nest. No default value.),
START_MONTH => qq(A list of MAX_DOM 2-digit integers specifying the starting UTC month of the simulation for each nest. No default value.),
START_DAY => qq(A list of MAX_DOM 2-digit integers specifying the starting UTC day of the simulation for each nest. No default value.),
START_HOUR => qq(A list of MAX_DOM 2-digit integers specifying the starting UTC hour of the simulation for each nest. No default value.),
END_YEAR => qq(A list of MAX_DOM 4-digit integers specifying the ending UTC year of the simulation for each nest. No default value.),
END_MONTH => qq(A list of MAX_DOM 2-digit integers specifying the ending UTC month of the simulation for each nest. No default value.),
END_DAY => qq(A list of MAX_DOM 2-digit integers specifying the ending UTC day of the simulation for each nest. No default value.),
END_HOUR => qq(A list of MAX_DOM 2-digit integers specifying the ending UTC hour of the simulation for each nest. No default value.),
START_DATE => qq(A list of MAX_DOM character strings of the form 'YYYY-MM-DD_HH:mm:ss' specifying the starting UTC date of the simulation for each nest. The start_date variable is an alternate to specifying start_year, start_month, start_day, and start_hour, and if both methods are used for specifying the starting time, the start_date variable will take precedence. No default value.),
END_DATE => qq(A list of MAX_DOM character strings of the form 'YYYY-MM-DD_HH:mm:ss' specifying the ending UTC date of the simulation for each nest. The end_date variable is an alternate to specifying end_year, end_month, end_day, and end_hour, and if both methods are used for specifying the ending time, the end_date variable will take precedence. No default value.),
INTERVAL_SECONDS => qq(The integer number of seconds between time-varying meteorological input files. No default value.),
ACTIVE_GRID => qq(A list of MAX_DOM logical values specifying, for each grid, whether that grid should be processed by geogrid and metgrid. Default value is .TRUE..),
IO_FORM_GEOGRID => qq(The WRF I/O API format that the domain files created by the geogrid program will be written in. Possible options are: 1 for binary; 2 for NetCDF; 3 for GRIB1. When option 1 is given, domain files will have a suffix of .int; when option 2 is given, domain files will have a suffix of .nc; when option 3 is given, domain files will have a suffix of .gr1. Default value is 2 (NetCDF).),
OPT_OUTPUT_FROM_GEOGRID_PATH => qq(A character string giving the path, either relative or absolute, to the location where output files from geogrid should be written to and read from. Default value is './'.),
DEBUG_LEVEL => qq(An integer value indicating the extent to which different types of messages should be sent to standard output. When debug_level is set to 0, only generally useful messages and warning messages will be written to standard output. When debug_level is greater than 100, informational messages that provide further runtime details are also written to standard output. Debugging messages and messages specifically intended for log files are never written to standard output, but are always written to the log files. Default value is 0.),
# GEOGRID section
PARENT_ID => qq(A list of MAX_DOM integers specifying, for each nest, the domain number of the nest’s parent; for the coarsest domain, this variable should be set to 1. Default value is 1.),
PARENT_GRID_RATIO => qq(A list of MAX_DOM integers specifying, for each nest, the nesting ratio relative to the domain’s parent. No default value.),
I_PARENT_START => qq(A list of MAX_DOM integers specifying, for each nest, the x-coordinate of the lower-left corner of the nest in the parent unstaggered grid. For the coarsest domain, a value of 1 should be specified. No default value.),
J_PARENT_START => qq(A list of MAX_DOM integers specifying, for each nest, the y-coordinate of the lower-left corner of the nest in the parent unstaggered grid. For the coarsest domain, a value of 1 should be specified. No default value.),
S_WE => qq(A list of MAX_DOM integers which should all be set to 1. Default value is 1.),
E_WE => qq(A list of MAX_DOM integers specifying, for each nest, the nest’s full west-east dimension. For nested domains, e_we must be one greater than an integer multiple of the nest's parent_grid_ratio (i.e., e_we = n*parent_grid_ratio+1 for some positive integer n). No default value.),
S_SN => qq(A list of MAX_DOM integers which should all be set to 1. Default value is 1.),
E_SN => qq(A list of MAX_DOM integers specifying, for each nest, the nest’s full south-north dimension. For nested domains, e_sn must be one greater than an integer multiple of the nest's parent_grid_ratio (i.e., e_sn = n*parent_grid_ratio+1 for some positive integer n). No default value.),
GEOG_DATA_RES => qq(A list of MAX_DOM character strings specifying, for each nest, a corresponding resolution or list of resolutions separated by + symbols of source data to be used when interpolating static terrestrial data to the nest’s grid. For each nest, this string should contain a resolution matching a string preceding a colon in a rel_path or abs_path specification (see the description of GEOGRID.TBL options) in the GEOGRID.TBL file for each field. If a resolution in the string does not match any such string in a rel_path or abs_path specification for a field in GEOGRID.TBL, a default resolution of data for that field, if one is specified, will be used. If multiple resolutions match, the first resolution to match a string in a rel_path or abs_path specification in the GEOGRID.TBL file will be used. Default value is 'default'.),
DX => qq(A real value specifying the grid distance in the x-direction where the map scale factor is 1. For ARW, the grid distance is in meters for the 'polar', 'lambert', and 'mercator' projection, and in degrees longitude for the 'lat-lon' projection; for NMM, the grid distance is in degrees longitude. Grid distances for nests are determined recursively based on values specified for parent_grid_ratio and parent_id. No default value.),
DY => qq(A real value specifying the nominal grid distance in the y-direction where the map scale factor is 1. For ARW, the grid distance is in meters for the 'polar', 'lambert', and 'mercator' projection, and in degrees latitude for the 'lat-lon' projection; for NMM, the grid distance is in degrees latitude. Grid distances for nests are determined recursively based on values specified for parent_grid_ratio and parent_id. No default value.),
MAP_PROJ => qq(A character string specifying the projection of the simulation domain. For ARW, accepted projections are 'lambert', 'polar', 'mercator', and 'lat-lon'; for NMM, a projection of 'rotated_ll' must be specified. Default value is 'lambert'.),
REF_LAT => qq(A real value specifying the latitude part of a (latitude, longitude) location whose (i,j) location in the simulation domain is known. For ARW, ref_lat gives the latitude of the center-point of the coarse domain by default (i.e., when ref_x and ref_y are not specified). For NMM, ref_lat always gives the latitude to which the origin is rotated. No default value.),
REF_LON => qq(A real value specifying the longitude part of a (latitude, longitude) location whose (i, j) location in the simulation domain is known. For ARW, ref_lon gives the longitude of the center-point of the coarse domain by default (i.e., when ref_x and ref_y are not specified). For NMM, ref_lon always gives the longitude to which the origin is rotated. For both ARW and NMM, west longitudes are negative, and the value of ref_lon should be in the range [-180, 180]. No default value.),
REF_X => qq(A real value specifying the i part of an (i, j) location whose (latitude, longitude) location in the simulation domain is known. The (i, j) location is always given with respect to the mass-staggered grid, whose dimensions are one less than the dimensions of the unstaggered grid. Default value is (((E_WE-1.)+1.)/2.) = (E_WE/2.).),
REF_Y => qq(A real value specifying the j part of an (i, j) location whose (latitude, longitude) location in the simulation domain is known. The (i, j) location is always given with respect to the mass-staggered grid, whose dimensions are one less than the dimensions of the unstaggered grid. Default value is (((E_SN-1.)+1.)/2.) = (E_SN/2.).),
TRUELAT1 => qq(A real value specifying, for ARW, the first true latitude for the Lambert conformal projection, or the only true latitude for the Mercator and polar stereographic projections. For NMM, truelat1 is ignored. No default value.),
TRUELAT2 => qq(A real value specifying, for ARW, the second true latitude for the Lambert conformal conic projection. For all other projections, truelat2 is ignored. No default value.),
STAND_LON => qq(A real value specifying, for ARW, the longitude that is parallel with the y-axis in the Lambert conformal and polar stereographic projections. For the regular latitude-longitude projection, this value gives the rotation about the earth's geographic poles. For NMM, stand_lon is ignored. No default value.),
POLE_LAT => qq(For the latitude-longitude projection for ARW, the latitude of the North Pole with respect to the computational latitude-longitude grid in which -90.0° latitude is at the bottom of a global domain, 90.0° latitude is at the top, and 180.0° longitude is at the center. Default value is 90.0.),
POLE_LON => qq(For the latitude-longitude projection for ARW, the longitude of the North Pole with respect to the computational lat/lon grid in which -90.0° latitude is at the bottom of a global domain, 90.0° latitude is at the top, and 180.0° longitude is at the center. Default value is 0.0.),
GEOG_DATA_PATH => qq(A character string giving the path, either relative or absolute, to the directory where the geographical data directories may be found. This path is the one to which rel_path specifications in the GEOGRID.TBL file are given in relation to. No default value.),
OPT_GEOGRID_TBL_PATH => qq(A character string giving the path, either relative or absolute, to the GEOGRID.TBL file. The path should not contain the actual file name, as GEOGRID.TBL is assumed, but should only give the path where this file is located. Default value is './geogrid/'.),
# UNGRIB section
OUT_FORMAT => qq(A character string set either to 'WPS', 'SI', or 'MM5'. If set to 'MM5', ungrib will write output in the format of the MM5 pregrid program; if set to 'SI', ungrib will write output in the format of grib_prep.exe; if set to 'WPS', ungrib will write data in the WPS intermediate format. Default value is 'WPS'.),
PREFIX => qq(A character string that will be used as the prefix for intermediate-format files created by ungrib; here, prefix refers to the string PREFIX in the filename PREFIX:YYYY-MM-DD_HH of an intermediate file. The prefix may contain path information, either relative or absolute, in which case the intermediate files will be written in the directory specified. This option may be useful to avoid renaming intermediate files if ungrib is to be run on multiple sources of GRIB data. Default value is 'FILE'.),
# METGRID section
FG_NAME => qq(A list of character strings specifying the path and prefix of ungribbed data files. The path may be relative or absolute, and the prefix should contain all characters of the filenames up to, but not including, the colon preceding the date. When more than one fg_name is specified, and the same field is found in two or more input sources, the data in the last encountered source will take priority over all preceding sources for that field. Default value is an empty list (i.e., no meteorological fields).),
CONSTANTS_NAME => qq(A list of character strings specifying the path and full filename of ungribbed data files which are time-invariant. The path may be relative or absolute, and the filename should be the complete filename; since the data are assumed to be time-invariant, no date will be appended to the specified filename. Default value is an empty list (i.e., no constant fields).),
IO_FORM_METGRID => qq(The WRF I/O API format that the output created by the metgrid program will be written in. Possible options are: 1 for binary; 2 for NetCDF; 3 for GRIB1. When option 1 is given, output files will have a suffix of .int; when option 2 is given, output files will have a suffix of .nc; when option 3 is given, output files will have a suffix of .gr1. Default value is 2 (NetCDF).),
OPT_OUTPUT_FROM_METGRID_PATH => qq(A character string giving the path, either relative or absolute, to the location where output files from metgrid should be written to. The default value is the current working directory (i.e., the default value is './').),
OPT_METGRID_TBL_PATH => qq(A character string giving the path, either relative or absolute, to the METGRID.TBL file; the path should not contain the actual file name, as METGRID.TBL is assumed, but should only give the path where this file is located. Default value is './metgrid/'.),
PROCESS_ONLY_BDY => qq(An integer specifying the number of boundary rows and columns to be processed by metgrid for time periods after the initial time; for the initial time, metgrid will always interpolate to every grid point. Setting this option to the intended value of spec_bdy_width in the WRF namelist.input will speed up processing in metgrid, but it should not be set if interpolated data are needed in the domain interior. If this option is set to zero, metgrid will horizontally interpolate meteorological data to every grid point in the model domains. This option is only available for ARW. Default value is 0.),
);
}
| enviroware/wps_help | wps_help.pl | Perl | mit | 18,892 |
{
=head1 NAME
Net::Google::Spelling - simple OOP-ish interface to the Google SOAP API for spelling suggestions
=head1 SYNOPSIS
use Net::Google::Spelling;
my $spelling = Net::Google::Spelling(\%args);
$spelling->phrase("muntreal qweebec");
print $spelling->suggest()."\n";
=head1 DESCRIPTION
Provides a simple OOP-ish interface to the Google SOAP API for
spelling suggestions.
This package is used by I<Net::Google>.
=cut
use strict;
package Net::Google::Spelling;
use base qw (Net::Google::tool);
use Carp;
$Net::Google::Spelling::VERSION = '1.0';
=head1 PACKAGE METHODS
=cut
=head2 $pkg = __PACKAGE__->new(\%args)
Valid arguments are :
=over 4
=item *
B<key>
I<string>.A Google API key.
If none is provided then the key passed to the parent I<Net::Google>
object will be used.
=item *
B<phrase>
I<string> or I<array reference>.
=item *
B<http_proxy>
I<url>. A URL for proxy-ing HTTP requests.
=item *
B<debug>
Valid options are:
=over 4
=item *
I<boolean>
If true prints debugging information returned by SOAP::Lite
to STDERR
=item *
I<coderef>.
Your own subroutine for munging the debugging information
returned by SOAP::Lite.
=back
=back
The object constructor in Net::Google 0.53, and earlier, expected
a I<GoogleSearchService> object as its first argument followed by
a hash reference of argument. Versions 0.6 and higher are backwards
compatible.
Returns an object. Woot!
=cut
sub new {
my $pkg = shift;
my $self = {};
bless $self,$pkg;
if (! $self->init(@_)) {
return undef;
}
return $self;
}
sub init {
my $self = shift;
my $args = $self->SUPER::init("spelling",@_)
|| return 0;
#
if ($args->{'phrase'}) {
defined($self->phrase( (ref($args->{'phrase'}) eq "ARRAY") ? @{$args->{'phrase'}} : $args->{'phrase'} )) || return 0;
}
return 1;
}
=head1 OBJECT METHODS
=cut
=head2 $obj->key($string)
Get/set the Google API key for this object.
=cut
# Defined in Net::Google::tool
=head2 $obj->http_proxy($url)
Get/set the HTTP proxy for this object.
Returns a string.
=cut
# Defined in Net::Google::tool
=head2 $obj->phrase(@words)
Add one or more words to the phrase you want to spell-check.
If the first item in I<@words> is empty, then any existing I<phrase>
data will be removed before the new data is added.
Returns a string. Returns undef if there was an error.
=cut
sub phrase {
my $self = shift;
my @words = @_;
if ((scalar(@words) > 1) && ($words[0] == "")) {
$self->{'_phrase'} = [];
}
if (@words) {
push @{$self->{'_phrase'}} , @words;
}
return join("",@{$self->{'_phrase'}});
}
=head2 $obj->suggest()
Fetch the spelling suggestion from the Google servers.
Returns a string. Returns undef if there was an error.
=cut
sub suggest {
my $self = shift;
$self->_queries(1);
return $self->{'_service'}->doSpellingSuggestion(
$self->key(),
$self->phrase(),
);
}
=head2 $obj->queries_exhausted()
Returns true or false depending on whether or not the current in-memory
B<session> has exhausted the Google API 1000 query limit.
=cut
# Defined in Net::Google::tool
=head1 VERSION
1.0
=head1 DATE
$Date: 2006/01/12 03:37:31 $
=head1 AUTHOR
Aaron Straup Cope
=head1 SEE ALSO
L<Net::Google>
=head1 LICENSE
Copyright (c) 2002-2005, Aaron Straup Cope. All Rights Reserved.
This is free software, you may use it and distribute it under the same
terms as Perl itself.
=cut
return 1;
}
| carlgao/lenga | images/lenny64-peon/usr/share/perl5/Net/Google/Spelling.pm | Perl | mit | 3,481 |
package O2CMS::Obj::Video;
# Class representing a video file
use strict;
use base 'O2::Obj::File';
#-------------------------------------------------------------------------------
sub canMove {
my ($obj, $fromContainer, $toContainer) = @_;
return 1; # can move to anywhere
}
#-------------------------------------------------------------------------------
1;
| haakonsk/O2-CMS | lib/O2CMS/Obj/Video.pm | Perl | mit | 366 |
package Google::Ads::AdWords::v201809::FunctionOperand;
use strict;
use warnings;
__PACKAGE__->_set_element_form_qualified(1);
sub get_xmlns { 'https://adwords.google.com/api/adwords/cm/v201809' };
our $XML_ATTRIBUTE_CLASS;
undef $XML_ATTRIBUTE_CLASS;
sub __get_attr_class {
return $XML_ATTRIBUTE_CLASS;
}
use base qw(Google::Ads::AdWords::v201809::FunctionArgumentOperand);
# Variety: sequence
use Class::Std::Fast::Storable constructor => 'none';
use base qw(Google::Ads::SOAP::Typelib::ComplexType);
{ # BLOCK to scope variables
my %FunctionArgumentOperand__Type_of :ATTR(:get<FunctionArgumentOperand__Type>);
my %value_of :ATTR(:get<value>);
__PACKAGE__->_factory(
[ qw( FunctionArgumentOperand__Type
value
) ],
{
'FunctionArgumentOperand__Type' => \%FunctionArgumentOperand__Type_of,
'value' => \%value_of,
},
{
'FunctionArgumentOperand__Type' => 'SOAP::WSDL::XSD::Typelib::Builtin::string',
'value' => 'Google::Ads::AdWords::v201809::Function',
},
{
'FunctionArgumentOperand__Type' => 'FunctionArgumentOperand.Type',
'value' => 'value',
}
);
} # end BLOCK
1;
=pod
=head1 NAME
Google::Ads::AdWords::v201809::FunctionOperand
=head1 DESCRIPTION
Perl data type class for the XML Schema defined complexType
FunctionOperand from the namespace https://adwords.google.com/api/adwords/cm/v201809.
A function operand in a matching function. Used to represent nested functions.
=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
| googleads/googleads-perl-lib | lib/Google/Ads/AdWords/v201809/FunctionOperand.pm | Perl | apache-2.0 | 1,787 |
#!/usr/bin/perl
use strict;
use warnings;
use CQS::ClassFactory;
use CQS::FileUtils;
use CQS::SystemUtils;
use CQS::ConfigUtils;
use CQS::UniqueTask;
use Test::More tests => 5;
my $config = {
general => {
task_name => "test",
cluster => "slurm",
},
"perl1" => {
class => "CQS::Perl",
perform => 1,
target_dir => "perl1",
option => "",
perlFile => "../SmallRNA/filterTrnaXml.py",
source => {
"test1" => [ "test1_1.zip", "test1_2.zip" ],
"test2" => [ "test2_1.zip", "test2_2.zip" ],
},
source_arg => "-i",
source_join_delimiter => ",",
output_to_same_folder => 1,
output_arg => "-o",
output_file_prefix => "",
output_file_ext => "._ITER_.1.fastq.gz",
output_other_ext => "._ITER_.2.fastq.gz",
iteration => 3,
sh_direct => 1,
pbs => {
"email" => "quanhu.sheng.1\@vumc.org",
"emailType" => "FAIL",
"nodes" => "1:ppn=1",
"walltime" => "10",
"mem" => "10gb"
},
},
"perl2" => {
class => "CQS::Perl",
perform => 1,
target_dir => "perl2",
option => "",
perlFile => "../SmallRNA/filterTrnaXml.py",
source_ref => ["perl1"],
source_arg => "-i",
source_join_delimiter => ",",
output_to_same_folder => 1,
output_arg => "-o",
output_file_prefix => "",
output_file_ext => "._ITER_.1.fastq.gz",
output_other_ext => "._ITER_.2.fastq.gz",
iteration => 3,
sh_direct => 1,
pbs => {
"email" => "quanhu.sheng.1\@vumc.org",
"emailType" => "FAIL",
"nodes" => "1:ppn=1",
"walltime" => "10",
"mem" => "10gb"
},
},
"r1" => {
class => "CQS::UniqueTask",
perform => 1,
target_dir => "r1",
option => "",
rtemplate => "../SmallRNA/filterTrnaXml.py",
source_ref => ["perl2"],
parameterSampleFile2_ref => ["perl1"],
output_file_ext => ".png;.csv",
sh_direct => 1,
pbs => {
"email" => "quanhu.sheng.1\@vumc.org",
"emailType" => "FAIL",
"nodes" => "1:ppn=1",
"walltime" => "10",
"mem" => "10gb"
},
},
sequencetask => {
class => "CQS::SequenceTaskSlurmSlim",
perform => 1,
target_dir => "sequencetask",
option => "",
source => {
#step1 => ["perl1", "perl2", "r1"],
step1 => [ "perl1", "r1" ],
},
sh_direct => 0,
cluster => "slurm",
pbs => {
"email" => "quanhu.sheng.1\@vumc.org",
"emailType" => "FAIL",
"nodes" => "1:ppn=1",
"walltime" => "10",
"mem" => "10gb"
},
}
};
my $test = CQS::UniqueTask->new();
#test result
eval {
$test->result( $config, "r1" );
};
ok($@, 'exception has been thrown');
like($@, qr/Override get_result_files/);
#test pbs
my $expect_pbs = {
'test' => 'r1/pbs/test.pbs',
};
my $actual_pbs = $test->get_pbs_files( $config, "r1" );
is_deeply( $actual_pbs, $expect_pbs );
#test get_pbs_source
my $expect_pbs_source = { "r1/pbs/test.pbs" => [ "test", "test1", "test2" ], };
my $actual_pbs_source = $test->get_pbs_source( $config, "r1" );
is_deeply( $actual_pbs_source, $expect_pbs_source );
#test result_pbs
my $expect_result_pbs_map = {
'test' => 'r1/pbs/test.pbs',
};
my $result_pbs_map = $test->get_result_pbs($config, "r1");
is_deeply( $result_pbs_map, $expect_result_pbs_map );
1;
| shengqh/ngsperl | test/CQS/TestUniqueTask.pl | Perl | apache-2.0 | 3,765 |
#
# Copyright 2019 Centreon (http://www.centreon.com/)
#
# Centreon is a full-fledged industry-strength solution that meets
# the needs in IT infrastructure and application monitoring for
# service performance.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
#
package apps::protocols::ospf::snmp::plugin;
use strict;
use warnings;
use base qw(centreon::plugins::script_snmp);
sub new {
my ($class, %options) = @_;
my $self = $class->SUPER::new(package => __PACKAGE__, %options);
bless $self, $class;
$self->{version} = '1.0';
%{$self->{modes}} = (
'neighbor' => 'apps::protocols::ospf::snmp::mode::neighbor',
);
return $self;
}
1;
__END__
=head1 PLUGIN DESCRIPTION
Check OSPF protocol in SNMP.
=cut
| Sims24/centreon-plugins | apps/protocols/ospf/snmp/plugin.pm | Perl | apache-2.0 | 1,286 |
=head1 TITLE
Add memoize into the standard library
=head1 VERSION
Maintainer: Adam Turoff <ziggy@panix.com>
Date: 14 Sep 2000
Last Modified: 18 Sep 2000
Mailing List: perl6-stdlib@perl.org
Number: 228
Version: 2
Status: Frozen
=head1 ABSTRACT
Caching through memoization is a very useful construct. It should be a
standard module.
=head1 DESCRIPTION
Memoization is a very useful technique to transparently cache
function return values. It can be used to quickly optimize
recursive functions, or functions that take a long time to
execute (such as gethostbyname).
A version of Memoize.pm should be added into the Perl6 standard
library, and it should be added as a pragmatic module (i.e. memoize.pm).
Adding Memoize plugins (Memoize::Expire, etc.) into the standard library
is a separate discussion.
=head1 NOTES ON FREEZE
There were no real objections to including memoize.pm in the Perl6 core.
=head1 OUTSTANDING ISSUES
A few people mentioned that using memoize() as a function has some
action-at-a-distance qualities, although it is useful for caching
builtin functions such as cos() and sin().
Bart Lateur mentioned that using a sub attribute would be logical:
sub foo :memoize {
}
While this does have merit, it does raise a few issues, such as being
able to turn on various Memoize extensions (such as expiry, tied
caches, etc.). On the other hand, this syntax does have merit for
using the default set of memoize options on a sub, without any
action-at-a-distance after effects.
These problems start to deal with language issues, such as being able
to use parameterized sub attributes, and internals issues, such as
being able to find sub attributes defined and implemented in an
extension. Neither of these are within the charter of perl6-stdlib
to figure out.
=head1 MIGRATION ISSUES
None.
=head1 IMPLEMENTATION
Add memoize into the perl6 source tarball, as a pragmatic module.
The Perl6 language may allow some workarounds to be avoided, such
as using a string value to specify the function to be memoized.
=head1 REFERENCES
Memoize.pm http://search.cpan.org/search?dist=Memoize
MiniMemoize from TPJ: http://perl.plover.com/MiniMemoize/memoize.html
Bart Lauter's commentary on a Perl6-ish way to memoize subs:
http://www.mail-archive.com/perl6-stdlib%40perl.org/msg00073.html
Leon Brocard's message on removing memoize's action-at-a-distance
nature: http://www.mail-archive.com/perl6-stdlib%40perl.org/msg00075.html
| autarch/perlweb | docs/dev/perl6/rfc/228.pod | Perl | apache-2.0 | 2,480 |
#
# 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 storage::ibm::ts2900::snmp::mode::hardware;
use base qw(centreon::plugins::templates::hardware);
sub set_system {
my ($self, %options) = @_;
$self->{cb_hook2} = 'snmp_execute';
$self->{thresholds} = {
default => [
['unknown', 'UNKNOWN'],
['ok', 'OK'],
['warning', 'WARNING'],
['failed', 'CRITICAL'],
['needClean', 'WARNING'], # for drive only
],
};
$self->{components_path} = 'storage::ibm::ts2900::snmp::mode::components';
$self->{components_module} = ['robot', 'drive', 'ctrl', 'ctrlpower', 'magazine'];
}
sub new {
my ($class, %options) = @_;
my $self = $class->SUPER::new(package => __PACKAGE__, %options, no_absent => 1, no_performance => 1, no_load_components => 1);
bless $self, $class;
$options{options}->add_options(arguments => {});
return $self;
}
sub snmp_execute {
my ($self, %options) = @_;
$self->{snmp} = $options{snmp};
my $oid_contStatusEntry = '.1.3.6.1.4.1.2.6.219.2.2.1.1';
my $oid_drvStatusEntry = '.1.3.6.1.4.1.2.6.219.2.2.2.1';
$self->{results} = $self->{snmp}->get_multiple_table(oids => [ { oid => $oid_contStatusEntry }, { oid => $oid_drvStatusEntry } ], return_type => 1);
}
1;
=head1 MODE
Check hardware.
=over 8
=item B<--component>
Which component to check (Default: '.*').
Can be: 'robot', 'drive', 'ctrl', 'ctrlpower', 'magazine'.
=item B<--filter>
Exclude some parts (comma seperated list)
Can also exclude specific instance: --filter=ctrl,1
=item B<--no-component>
Return an error if no compenents are checked.
If total (with skipped) is 0. (Default: 'critical' returns).
=item B<--threshold-overload>
Set to overload default threshold values (syntax: section,[instance,]status,regexp)
It used before default thresholds (order stays).
Example: --threshold-overload='drive,OK,needClean'
=back
=cut
package storage::ibm::ts2900::snmp::mode::components::common;
my %map_default_status = (1 => 'unknown', 2 => 'ok', 3 => 'warning', 4 => 'failed');
sub check {
my ($self, %options) = @_;
$self->{output}->output_add(long_msg => "Checking " . $options{description});
$self->{components}->{$options{section}} = {name => $options{section}, total => 0, skip => 0};
return if ($self->check_filter(section => $options{section}));
foreach my $oid ($self->{snmp}->oid_lex_sort(keys %{$self->{results}})) {
next if ($oid !~ /^$options{mapping}->{$options{status}}->{oid}\.(.*)$/);
my $instance = $1;
my $result = $self->{snmp}->map_instance(mapping => $options{mapping}, results => $self->{results}, instance => $instance);
next if ($self->check_filter(section => $options{section}, instance => $instance));
$self->{components}->{$options{section}}->{total}++;
$self->{output}->output_add(long_msg => sprintf("%s '%s' status is '%s' [instance = %s]",
$options{description}, $instance, $result->{$options{status}}, $instance));
my $exit = $self->get_severity(label => 'default', section => $options{section}, value => $result->{$options{status}});
if (!$self->{output}->is_status(value => $exit, compare => 'ok', litteral => 1)) {
$self->{output}->output_add(severity => $exit,
short_msg => sprintf("%s '%s' status is '%s'", $options{description}, $instance, $result->{$options{status}}));
}
}
}
package storage::ibm::ts2900::snmp::mode::components::robot;
use strict;
use warnings;
my $mapping_robot = {
robotStatus => { oid => '.1.3.6.1.4.1.2.6.219.2.2.1.1.6', map => \%map_default_status },
};
sub load {}
sub check {
my ($self) = @_;
storage::ibm::ts2900::snmp::mode::components::common::check($self,
section => 'robot', mapping => $mapping_robot, description => 'robot', status => 'robotStatus');
}
package storage::ibm::ts2900::snmp::mode::components::ctrl;
use strict;
use warnings;
my $mapping_ctrl = {
contState => { oid => '.1.3.6.1.4.1.2.6.219.2.2.1.1.7', map => \%map_default_status },
};
sub load {}
sub check {
my ($self) = @_;
storage::ibm::ts2900::snmp::mode::components::common::check($self,
section => 'ctrl', mapping => $mapping_ctrl, description => 'controller', status => 'contState');
}
package storage::ibm::ts2900::snmp::mode::components::ctrlpower;
use strict;
use warnings;
my $mapping_ctrlpower = {
contPowerStatus => { oid => '.1.3.6.1.4.1.2.6.219.2.2.1.1.2', map => \%map_default_status },
};
sub load {}
sub check {
my ($self) = @_;
storage::ibm::ts2900::snmp::mode::components::common::check($self,
section => 'ctrlpower', mapping => $mapping_ctrlpower, description => 'controller power', status => 'contPowerStatus');
}
package storage::ibm::ts2900::snmp::mode::components::magazine;
use strict;
use warnings;
my $mapping_magazine = {
magStatus => { oid => '.1.3.6.1.4.1.2.6.219.2.2.1.1.4', map => \%map_default_status },
};
sub load {}
sub check {
my ($self) = @_;
storage::ibm::ts2900::snmp::mode::components::common::check($self,
section => 'magazine', mapping => $mapping_magazine, description => 'magazine', status => 'magStatus');
}
package storage::ibm::ts2900::snmp::mode::components::drive;
use strict;
use warnings;
my %map_drive_status = (1 => 'unknown', 2 => 'ok', 3 => 'needClean', 4 => 'warning', 5 => 'failed');
my $mapping_drive = {
driveStatus => { oid => '.1.3.6.1.4.1.2.6.219.2.2.2.1.3', map => \%map_drive_status },
};
sub load {}
sub check {
my ($self) = @_;
storage::ibm::ts2900::snmp::mode::components::common::check($self,
section => 'drive', mapping => $mapping_drive, description => 'drive', status => 'driveStatus');
}
| Tpo76/centreon-plugins | storage/ibm/ts2900/snmp/mode/hardware.pm | Perl | apache-2.0 | 6,601 |
use strict;
use warnings;
use Getopt::Long;
use Pod::Usage;
use Bio::EnsEMBL::Compara::Production::Projection::RunnableDB::ProjectOntologyXref;
use Bio::EnsEMBL::Compara::Production::Projection::RunnableDB::RunnableLogger;
use Bio::EnsEMBL::Registry;
my $log_config = <<LOGCFG;
log4perl.logger=DEBUG, Screen
log4perl.appender.Screen=Log::Log4perl::Appender::Screen
log4perl.appender.Screen.stderr=1
log4perl.appender.Screen.Threshold=DEBUG
log4perl.appender.Screen.layout=Log::Log4perl::Layout::PatternLayout
log4perl.appender.Screen.layout.ConversionPattern=%d %p> %M{2}::%L - %m%n
LOGCFG
my @options = qw(
source=s
target=s
engine=s
compara=s
source_name=s
write_to_db
display_xrefs
all_sources
one_to_many
file=s
registry=s
log_cfg=s
verbose help man
);
#The only thing we run in global
run();
#End of the script
sub run {
my $opts = _get_opts();
_initalise_log($opts);
my $runnable = _build_runnable($opts);
$runnable->run_without_hive();
return;
}
sub _get_opts {
my $opts = {};
GetOptions($opts, @options) or pod2usage(1);
pod2usage( -exitstatus => 0, -verbose => 1 ) if $opts->{help};
pod2usage( -exitstatus => 0, -verbose => 2 ) if $opts->{man};
#Source & target check
_exit('No -source option given', 1, 1) if ! $opts->{source};
_exit('No -target option given', 1, 1) if ! $opts->{target};
_exit('No -compara option given', 1, 1) if ! $opts->{compara};
#Registry work
my $reg = $opts->{registry};
_exit('No -registry option given', 2, 1) if ! $reg && ! -f $reg;
my @args = ($reg);
push @args, 1 if $opts->{verbose};
Bio::EnsEMBL::Registry->load_all(@args);
#Engine work
if(! $opts->{engine}) {
my $base = 'Bio::EnsEMBL::Compara::Production::Projection::';
if($opts->{display_xrefs}) {
$opts->{engine} = $base.'DisplayXrefProjectionEngine';
}
else {
$opts->{engine} = $base.'GOAProjectionEngine';
}
}
if(! $opts->{write_to_db} && ! $opts->{file}) {
_exit('-write_to_db and -file were not specified. We need one', 3, 1);
}
return $opts;
}
sub _build_runnable {
my ($opts) = @_;
my %args = (
-PROJECTION_ENGINE => _build_engine($opts),
-TARGET_GENOME_DB => _get_genome_db($opts, $opts->{target}),
-DEBUG => $opts->{verbose}
);
$args{-FILE} = $opts->{file} if $opts->{file};
$args{-WRITE_DBA} = _get_adaptor($opts->{target}, 'core') if $opts->{write_to_db};
return Bio::EnsEMBL::Compara::Production::Projection::RunnableDB::ProjectOntologyXref->new_without_hive(%args);
}
sub _build_engine {
my ($opts) = @_;
my $mod = $opts->{engine};
_runtime_import($mod, 1);
my %args = (
-GENOME_DB => _get_genome_db($opts, $opts->{source}),
-DBA => _get_adaptor($opts->{compara}, 'compara'),
_log()
);
$args{-ALL_SOURCES} = 1 if $opts->{all_sources};
$args{-ONE_TO_MANY} = 1 if $opts->{one_to_many};
$args{-SOURCE} = $opts->{source_name} if $opts->{source_name};
return $mod->new(%args);
}
sub _get_genome_db {
my ($opts, $name) = @_;
my $compara_dba = _get_adaptor($opts->{compara}, 'compara');
my $core_dba = _get_adaptor($name, 'core');
my $gdb_a = $compara_dba->get_GenomeDBAdaptor();
my $gdb = $gdb_a->fetch_by_core_DBAdaptor($core_dba);
return $gdb;
}
sub _get_adaptor {
my ($name, $group) = @_;
my $dba = Bio::EnsEMBL::Registry->get_DBAdaptor($name, $group);
if(! defined $dba) {
_exit("No adaptor for ${name} and ${group}. Check your registry and try again", 5, 1);
}
return $dba;
}
sub _exit {
my ($msg, $status, $verbose) = @_;
print STDERR $msg, "\n";
pod2usage( -exitstatus => $status, -verbose => $verbose);
}
my $log4perl_available = 0;
sub _initalise_log {
my ($opts) = @_;
if(_runtime_import('Log::Log4perl')) {
if($opts->{log_cfg}) {
Log::Log4perl->init($opts->{log_cfg});
}
else {
Log::Log4perl->init(\$log_config);
}
$log4perl_available = 1;
}
}
#If log4perl was available let the module get it's own logger otherwise we
#build our own
sub _log {
my ($opts) = @_;
if($log4perl_available) {
return;
}
my $log = Bio::EnsEMBL::Compara::Production::Projection::RunnableDB::RunnableLogger->new(
-DEBUG => $opts->{verbose}
);
return ( -LOG => $log );
}
sub _runtime_import {
my ($mod, $die) = @_;
eval "require ${mod}";
_exit "Cannot import ${mod}: $@", 5, 1 if $die && $@;
return ($@) ? 0 : 1;
}
__END__
=pod
=head1 NAME
project_dbentry.pl
=head1 SYNOPSIS
./project_dbentry.pl -registry REG -source SRC -target TRG -compara COM [-log_cfg LOC] -display_xrefs] [-engine ENG] [-write_to_db] [-file FILE] [-verbose] [-help | -man]
=head1 DESCRIPTION
This script is a thin-wrapper around the RunnableDB instance and is used
for the ad-hoc testing & running of the Xref projection engine. At the moment
this is configured for projecting GO terms from one species to another
however it will operate on any Xref so long as you can provide the correct
projection engine implementation.
The script can also add data back into a database but to do so we must
assume that a core DBAdaptor for the target species is linked to
a read/write account. Otherwise you will not be able to perform the
linkage.
For a flavor of what the pipeline can do pass the script a file name which
will produce a CSV of what I<would> have been written back to the DB.
=head1 OPTIONS
=over 8
=item B<--registry>
The registry to use
=item B<--source>
The source species (species with GOs)
=item B<--target>
The target species (species without GOs)
=item B<--compara>
The compara database to use
=item B<--log_cfg>
The log4perl configuration location; otherwise the code will use a default
logger to STDERR
=item B<--source_name>
Optional argument allowing the specification of the level to perform
projections at. This means if we wish to project from Gene to Gene you can
specify ENSEMBLGENE (these are the same names as used in MEMBER). The default
is ENSEMBLPEP and is the recommended mode.
=item B<--engine>
The engine to use; defaults to GOAProjectionEngine or
DisplayXrefProjectionEngine. Must be a fully qualified package
=item B<--display_xrefs>
Flags we wish to project display Xrefs
=item B<--all_sources>
Allow the input of any sources of information
=item B<--one_to_many>
Bring in 1:m relationships rather than just 1:1
=item B<--write_to_db>
Indicates we want Xrefs going back to the core DB. If used we assume the
registry's core DBAdaptor is writable
=item B<--file>
Location to write output to. Can be a directory (so an automatically
generated name will be given) or a full path. Specifying B<-> will write the
file out to STDOUT.
=item B<--verbose>
Start emitting more messages
=item B<--help>
Basic help with options
=item B<--man>
Manual version of the help. More complete
=back
=head1 REQUIREMENTS
=over 8
=item EnsEMBL core (v60+)
=item EnsEMBL compara
=item EnsEMBL hive
=item Log::Log4perl - if not present on PERL5LIB or @INC messages go to STDOUT
=item Text::CSV (for file writing)
=item Data::Predicate
=back
=cut | adamsardar/perl-libs-custom | EnsemblAPI/ensembl-compara/scripts/projection/project_dbentry.pl | Perl | apache-2.0 | 7,058 |
#
# Copyright 2015 Electric Cloud, Inc.
#
# 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.
#
#########################
## createcfg.pl
#########################
use ElectricCommander;
use ElectricCommander::PropDB;
my $opts;
my $PLUGIN_NAME = "EC-Gerrit";
if (!defined $PLUGIN_NAME) {
print "PLUGIN_NAME must be defined\n";
exit 1;
}
## get an EC object
my $ec = new ElectricCommander();
$ec->abortOnError(0);
## load option list from procedure parameters
my $x = $ec->getJobDetails($ENV{COMMANDER_JOBID});
my $nodeset = $x->find('//actualParameter');
foreach my $node ($nodeset->get_nodelist) {
my $parm = $node->findvalue('actualParameterName');
my $val = $node->findvalue('value');
$opts->{$parm}="$val";
}
if (!defined $opts->{config} || "$opts->{config}" eq "" ) {
print "config parameter must exist and be non-blank\n";
exit 1;
}
# check to see if a config with this name already exists before we do anything else
my $xpath = $ec->getProperty("/myProject/gerrit_cfgs/$opts->{config}");
my $property = $xpath->findvalue("//response/property/propertyName");
if (defined $property && $property ne "") {
my $errMsg = "A configuration named '$opts->{config}' already exists.";
$ec->setProperty("/myJob/configError", $errMsg);
print $errMsg;
exit 1;
}
my $cfg = new ElectricCommander::PropDB($ec,"/myProject/gerrit_cfgs");
# add all the options as properties
foreach my $key (keys % {$opts}) {
if ($key eq "config" ) {
next;
}
$cfg->setCol("$opts->{config}","$key","$opts->{$key}");
}
exit 0;
| electric-cloud/EC-Gerrit | src/main/resources/project/config/createcfg.pl | Perl | apache-2.0 | 2,074 |
#!/usr/bin/perl -w
use strict;
use warnings;
my $dir = "/home/yi/data/DNA_Methylation/Methy_ZhouYi/RData/t_test/";
open(HYPO,$dir."hypo.txt") or die "$!\n";
<HYPO>;
my @hypo_list = <HYPO>;
close(HYPO);
open(OUTPUT,">".$dir."hypo_new") or die "$!\n";
print OUTPUT "IlmnID"."\t"."Methy_p"."\t"."Entrez"."\t"."Refseq"."\t"."Gene group"."\t"."Relation to CpG"."\n";
foreach my $row(@hypo_list)
{
my @a = split("\t", $row);
#chomp $a[2];
#chomp $a[3];
#chomp $a[4];
my @Entrez = split(";",$a[2]);
my @Refseq = split(";",$a[3]);
my @Gene_group = split(";",$a[4]);
if($a[2] =~ m/;/)
{
my $length = scalar @Entrez;
for(my $i=0;$i<$length;$i++)
{
print OUTPUT $a[0]."\t".$a[1]."\t".$Entrez[$i]."\t".$Refseq[$i]."\t".$Gene_group[$i]."\t".$a[5]."\n";
}
}
else
{
print OUTPUT $a[0]."\t".$a[1]."\t".$a[2]."\t".$a[3]."\t".$a[4]."\t".$a[5];
}
}
close(OUTPUT); | SCP-028/UGA | archive/DNA_Methylation/Name_convertion/stretch_extrez.pl | Perl | apache-2.0 | 910 |
#
# 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 network::cisco::firepower::fxos::snmp::mode::components::memoryunit;
use strict;
use warnings;
use network::cisco::firepower::fxos::snmp::mode::components::resources qw($map_operability);
my $mapping = {
dn => { oid => '.1.3.6.1.4.1.9.9.826.1.50.11.1.2' }, # cfprMemoryUnitDn
operability => { oid => '.1.3.6.1.4.1.9.9.826.1.50.11.1.18', map => $map_operability } # cfprMemoryUnitOperability
};
my $mapping_stats = {
dn => { oid => '.1.3.6.1.4.1.9.9.826.1.50.12.1.2' }, # cfprMemoryUnitEnvStatsDn
temperature => { oid => '.1.3.6.1.4.1.9.9.826.1.50.12.1.7' } # cfprMemoryUnitEnvStatsTemperatureAvg
};
sub load {
my ($self) = @_;
push @{$self->{request}}, map({ oid => $_->{oid} }, values(%$mapping), values(%$mapping_stats));
}
sub check {
my ($self) = @_;
$self->{output}->output_add(long_msg => 'checking memory units');
$self->{components}->{memoryunit} = { name => 'memory units', total => 0, skip => 0 };
return if ($self->check_filter(section => 'memoryunit'));
my $results = { map(%{$self->{results}->{ $_->{oid} }}, values(%$mapping)) };
my $results_stats = { map(%{$self->{results}->{ $_->{oid} }}, values(%$mapping_stats)) };
my ($exit, $warn, $crit, $checked);
foreach my $oid ($self->{snmp}->oid_lex_sort(keys %$results)) {
next if ($oid !~ /^$mapping->{operability}->{oid}\.(.*)$/);
my $result = $self->{snmp}->map_instance(mapping => $mapping, results => $results, instance => $1);
next if ($self->check_filter(section => 'memoryunit', instance => $result->{dn}));
$self->{components}->{memoryunit}->{total}++;
my $result_stats = $self->compare_dn(
regexp => "^$result->{dn}/",
lookup => 'dn',
results => $results_stats,
mapping => $mapping_stats
);
$self->{output}->output_add(
long_msg => sprintf(
"memory unit '%s' status is '%s' [temperature: %s C].",
$result->{dn},
$result->{operability},
defined($result_stats->{temperature}) ? $result_stats->{temperature} : '-'
)
);
$exit = $self->get_severity(label => 'operability', section => 'memoryunit', instance => $result->{dn}, value => $result->{operability});
if (!$self->{output}->is_status(value => $exit, compare => 'ok', litteral => 1)) {
$self->{output}->output_add(
severity => $exit,
short_msg => sprintf(
"memory unit '%s' status is '%s'",
$result->{dn},
$result->{operability}
)
);
}
next if (!defined($result_stats->{temperature}));
($exit, $warn, $crit, $checked) = $self->get_severity_numeric(section => 'memoryunit.temperature', instance => $result->{dn}, value => $result_stats->{temperature});
if (!$self->{output}->is_status(value => $exit, compare => 'ok', litteral => 1)) {
$self->{output}->output_add(
severity => $exit,
short_msg => sprintf(
"memory unit '%s' temperature is %s C",
$result->{dn},
$result_stats->{temperature}
)
);
}
$self->{output}->perfdata_add(
nlabel => 'hardware.memoryunit.temperature.celsius',
unit => 'C',
instances => $result->{dn},
value => $result_stats->{temperature},
warning => $warn,
critical => $crit
);
}
}
1;
| Tpo76/centreon-plugins | network/cisco/firepower/fxos/snmp/mode/components/memoryunit.pm | Perl | apache-2.0 | 4,402 |
# Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
# Copyright [2016-2018] 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.
package Bio::EnsEMBL::Analysis::RunnableDB::Finished::ClusterDepthFilter;
use warnings ;
use strict;
use Bio::EnsEMBL::Analysis::Config::General;
use Bio::EnsEMBL::SimpleFeature;
use Bio::EnsEMBL::Utils::Exception qw(verbose throw warning);
use Bio::EnsEMBL::Pipeline::Tools::MM_Taxonomy;
use Data::Dumper;
#use Scalar::Util 'weaken';
use base 'Bio::EnsEMBL::Analysis::RunnableDB::Finished::DepthFilter';
my $DEBUG = 0;
my $SANITY_CHECK_STRANDS = 0;
# NB: not a method
sub overlap {
# check if feature f1 overlaps feature f2
my ( $f1_start, $f1_end, $f2_start, $f2_end ) = @_;
return ($f1_end >= $f2_start and $f1_start <= $f2_end);
}
# NB: not a method
sub is_consistent {
# check if the given hit can join the cluster
my $hit = shift;
my $cluster = shift;
# check if any of the new hit's exons encroach on any
# of the cluster's introns
for my $af ( @{ $hit->{features} } ) {
for my $intron ( @{ $cluster->{introns} } ) {
if ( overlap( $af->start, $af->end, $intron->[0], $intron->[1] ) ) {
return 0;
}
}
}
# check if any of the clusters's exons encroach on any
# of the new hit's introns
my $start = $cluster->{start};
for my $cluster_intron ( @{ $cluster->{introns} } ) {
my $end = $cluster_intron->[0]-1;
for my $intron ( @{ $hit->{introns} } ) {
if ( overlap( $start, $end, $intron->[0], $intron->[1] ) ) {
return 0;
}
}
$start = $cluster_intron->[1]+1;
}
my $end = $cluster->{end};
for my $intron ( @{ $hit->{introns} } ) {
if ( overlap( $start, $end, $intron->[0], $intron->[1] ) ) {
return 0;
}
}
return 1;
}
# NB: not a method
sub find_new_introns {
# identify and return any introns from set2 that are not in set1
my ( $set1, $set2 ) = @_;
my %h1 = map { $_->[0] . "-" . $_->[1] => $_ } @$set1;
my %h2 = map { $_->[0] . "-" . $_->[1] => $_ } @$set2;
my @new_keys = grep { !( exists $h1{$_} ) } keys %h2;
return [ map { $h2{$_} } @new_keys ];
}
# NB: not a method
sub hit_str {
my $hit = shift;
my $s = '';
map { $s .= $_->start . "-" . $_->end . "," } @{ $hit->{features} };
$s .= " (".$hit->{taxon_id}.")";
return $s;
}
# NB: not a method
sub cluster_str {
my $cluster = shift;
my $s = $cluster->{start} . "-";
map { $s .= $_->[0] . "," . $_->[1] . "-" } @{ $cluster->{introns} };
$s .= $cluster->{end};
return $s;
}
# NB: not a method
sub meta_cluster_str {
my $meta = shift;
my $s = sprintf "%d-%d (%d)", $meta->{start}, $meta->{end}, $meta->{strand};
return $s;
}
sub group_features_by_name {
my ( $self, $orig_features, $percentid_cutoff, $no_filter ) = @_;
my %grouped_by_name = ();
for my $af (@$orig_features) {
my ( $score, $percentid ) = ( $af->score(), $af->percent_id() );
if ( $percentid < $percentid_cutoff ) {
next;
}
my $hit = $grouped_by_name{ $af->hseqname() } ||= {};
push @{ $hit->{features} }, $af;
if ( $no_filter && $self->get_hit_description( $af->hseqname() ) ) {
$hit->{taxon_id} =
$self->get_hit_description( $af->hseqname() )->taxon_id;
}
}
return \%grouped_by_name;
}
sub break_discontinuities {
my ( $self, $hits_by_name, $no_filter, $slice ) = @_;
my @hits = ();
for my $hit ( values %$hits_by_name ) {
print STDERR "ClusterDepthFilter: Processing hit: ", $hit->{features}->[0]->hseqname,
"\n"
if $DEBUG;
my @remaining_features = sort { $a->hstrand <=> $b->hstrand
||
$a->start <=> $b->start
||
$a->hstart <=> $b->hstart } @{ $hit->{features} };
while (@remaining_features) {
my @features = @remaining_features;
@remaining_features = ();
my $last = shift @features;
my $new_hit = {};
$new_hit->{features} = [$last];
$new_hit->{tot_score} = $last->score;
$new_hit->{avg_percentid} = $last->percent_id;
$new_hit->{strand} = $last->hstrand;
$new_hit->{taxon_id} = $hit->{taxon_id} if $no_filter;
print STDERR "ClusterDepthFilter: starting new hit: hstrand: ",
$last->hstrand, " af: ", $last->hstart, "-", $last->hend,
" (", $last->start, "-", $last->end, ")\n"
if $DEBUG;
FEAT: for my $af ( @features ) {
if ( $last->hstrand == $af->hstrand
&& $last->hstart == $af->hstart
&& $last->hend == $af->hend
&& $last->start == $af->start
&& $last->end == $af->end ) {
print STDERR "ClusterDepthFilter: Found duplicate align "
. "feature for hit " . $af->hseqname
. " [coords: " . $af->hstart . "-" . $af->hend
. " (" . $af->start . "-" . $af->end . ")"
. ", slice: "
. $slice->name . "]\n";
next FEAT;
}
my $delta =
$af->hstrand == $af->strand
? ( $af->hstart - $last->hend )
: ( $last->hstart - $af->hend );
if ( $af->hstrand == $last->hstrand && $af->start <= $last->end ) {
# found an overlap - bump for reprocessing
print STDERR "ClusterDepthFilter: found overlap: hstrand: ",
$af->hstrand, " last: ", $last->hstart, "-", $last->hend,
" (", $last->start, "-", $last->end, ") af: ", $af->hstart,
"-", $af->hend, " (", $af->start, "-", $af->end, ")\n"
if $DEBUG;
push @remaining_features, $af;
next FEAT;
}
elsif ( $last->hstrand != $af->hstrand || $delta != 1 ) {
# found a discontinuity - it might belong to stuff on remaining features
print STDERR "ClusterDepthFilter: discontinuity: hstrand: ",
$af->hstrand, " last: ", $last->hstart, "-", $last->hend,
" (", $last->start, "-", $last->end, ") af: ", $af->hstart,
"-", $af->hend, " (", $af->start, "-", $af->end, ")\n"
if $DEBUG;
push @remaining_features, $af;
next FEAT;
}
else {
print STDERR "ClusterDepthFilter: continuing hit: hstrand: ",
$af->hstrand, " last: ", $last->hstart, "-", $last->hend,
" (", $last->start, "-", $last->end, ") af: ", $af->hstart,
"-", $af->hend, " (", $af->start, "-", $af->end, ")\n"
if $DEBUG;
# continue the same hit
push @{ $new_hit->{features} }, $af;
$new_hit->{tot_score} += $af->score;
$new_hit->{avg_percentid} += $af->percent_id;
}
$last = $af;
}
# add the hit to the list
$new_hit->{avg_percentid} /= scalar( @{ $new_hit->{features} } );
push @hits, $new_hit;
if (@remaining_features) {
print STDERR "ClusterDepthFilter: rescanning\n" if $DEBUG;
}
} # @remaining_features
}
return \@hits;
}
sub cluster_hits {
my ( $self, $hits ) = @_;
# sort the hits so they are arranged sequentially against the
# genomic sequence, with the longest sequence first for hits
# with identical starts (this allows us to find all overlaps in
# one pass)
my @hits = sort {
( $a->{features}->[0]->start <=> $b->{features}->[0]->start )
|| ( $b->{features}->[-1]->end <=> $a->{features}->[-1]->end )
} @$hits;
# try to cluster hits according to overlaps and introns
my @clusters = ();
for my $hit (@hits) {
my @afs = @{ $hit->{features} };
$hit->{start} = $afs[0]->start;
$hit->{end} = $afs[-1]->end;
print STDERR "ClusterDepthFilter: looking at hit: ", hit_str($hit), "\n"
if $DEBUG;
my @introns = ();
if ( @afs > 1 ) { # we have at least 1 intron
# identify all the introns
my $start = $afs[0]->end;
for my $af ( @afs[ 1 .. $#afs - 1 ] ) {
my $end = $af->start;
push @introns, [ $start+1, $end-1 ];
$start = $af->end;
}
my $end = $afs[-1]->start;
push @introns, [ $start+1, $end-1 ];
}
$hit->{introns} = [@introns];
# check if we can add this hit to any existing cluster
my $added = 0;
for my $cluster (@clusters) {
if ( $hit->{strand} == $cluster->{strand}
&& $hit->{start} >= $cluster->{start}
&& $hit->{end} <= $cluster->{end}
&& is_consistent( $hit, $cluster ) )
{
# this hit is subsumed by the cluster and its
# introns are consistent, so we can add it
print STDERR "ClusterDepthFilter: adding hit to cluster: ",
cluster_str($cluster), "\n"
if $DEBUG;
push @{ $cluster->{hits} }, $hit;
$added = 1;
last;
}
else {
print STDERR "ClusterDepthFilter: can't add hit to cluster: ",
cluster_str($cluster), "\n"
if $DEBUG;
}
}
# if we didn't find a matching cluster, start a new one
if ( !$added ) {
my $cluster = {
start => $hit->{start},
end => $hit->{end},
introns => [ map { [@$_] } @introns ],
hits => [$hit],
strand => $hit->{strand}
};
push @clusters, $cluster;
print STDERR "ClusterDepthFilter: creating new cluster: ",
cluster_str($cluster), "\n"
if $DEBUG;
}
}
return \@clusters;
}
sub compute_vulgar_strings {
my $hits = shift;
for my $hit (@$hits) {
my @afs = @{ $hit->{features} };
my $vs = '';
my $last;
for my $af (@afs) {
if ($last) {
$vs .= '5 0 2 ';
$vs .= 'I 0 '.($af->start - $last - 4).' ';
$vs .= '3 0 2 ';
}
$vs .= 'M '.$af->length.' '.$af->length.' ';
$last = $af->end;
}
$hit->{vulgar_string} = $vs;
#print STDERR hit_str($hit), "\n\n";
#print STDERR $vs, "\n\n";
}
}
sub is_consistent_by_vulgar_string {
my ($hit, $cluster) = @_;
return 1 unless ($hit->{vulgar_string} =~ /I/ || $cluster->{vulgar_string} =~ /I/);
my $vs = $hit->{vulgar_string};
$vs =~ s/^M \d+ \d+ 5 0 2 //;
$vs =~ s/ 3 0 2 M \d+ \d+ $//;
if ($cluster->{vulgar_string} =~ /$vs/) {
if ($vs ne $hit->{vulgar_string}) {
print STDERR "orig : ", $hit->{vulgar_string}, "\n";
print STDERR "trimmed: ", $vs, "\n";
}
print STDERR "MATCH:\n";
print STDERR $vs, "\n";
print STDERR $cluster->{vulgar_string}, "\n";
return 1;
}
else {
print STDERR "NO MATCH:\n";
print STDERR $vs, "\n";
print STDERR $cluster->{vulgar_string}, "\n";
return 0;
}
}
sub cluster_hits_by_strings {
my $self = shift;
my $hits = shift;
compute_vulgar_strings($hits);
my @hits = sort {
( $a->{features}->[0]->start <=> $b->{features}->[0]->start )
|| ( $b->{features}->[-1]->end <=> $a->{features}->[-1]->end )
} @$hits;
my @clusters = ();
for my $hit (@hits) {
my $added = 0;
for my $cluster (@clusters) {
if ( $hit->{strand} == $cluster->{strand}
&& $hit->{start} >= $cluster->{start}
&& $hit->{end} <= $cluster->{end}
&& is_consistent_by_vulgar_string( $hit, $cluster ) )
{
push @{ $cluster->{hits} }, $hit;
$added = 1;
last;
}
}
# if we didn't find a matching cluster, start a new one
if ( !$added ) {
my $cluster = {
start => $hit->{start},
end => $hit->{end},
vulgar_string => $hit->{vulgar_string},
hits => [$hit],
strand => $hit->{strand}
};
push @clusters, $cluster;
print STDERR "ClusterDepthFilter: creating new cluster: ",
cluster_str($cluster), "\n"
if $DEBUG;
}
}
print "Created ",scalar(@clusters), " clusters using vulgar strings\n";
return @clusters;
}
sub cluster_clusters {
# cluster the clusters by overlaps
my ( $self, $clusters ) = @_;
my @meta_clusters = ();
for my $cluster (@$clusters) {
my $added = 0;
for my $meta (@meta_clusters) {
if (
overlap(
$cluster->{start}, $cluster->{end},
$meta->{start}, $meta->{end}
)
&& $cluster->{strand} == $meta->{strand}
)
{
push @{ $meta->{clusters} }, $cluster;
$added = 1;
last;
}
}
if ( !$added ) {
my $new_meta = {
start => $cluster->{start},
end => $cluster->{end},
strand => $cluster->{strand},
clusters => [$cluster],
hits_added => 0
};
push @meta_clusters, $new_meta;
}
}
return \@meta_clusters;
}
sub build_summary_features {
my ( $self, $meta_clusters ) = @_;
my @summary_features = ();
my $tot_filtered = 0;
for my $meta_cluster (@$meta_clusters) {
for my $cluster ( @{ $meta_cluster->{clusters} } ) {
# create new 'summary' features representing the maximal
# coverage of the remaining features (if we have any)
# establish the start, end, introns list and score of
# the summary feature
my ( $start, $end, $score, $introns );
my $filtered = 0;
for my $hit ( @{ $cluster->{hits} } ) {
# ignore hits that have already been added
if ( $hit->{features}->[0]->analysis == $self->analysis ) {
print STDERR
"ClusterDepthFilter: ignoring previously added feature\n"
if $DEBUG;
next;
}
if ( defined $start ) {
# check if this hit extends the summary feature
my $s = $hit->{features}->[0]->start;
$start = $s if $s < $start;
my $e = $hit->{features}->[-1]->end;
$end = $e if $e > $end;
my $ms = $hit->{tot_score};
$score = $ms if $ms > $score;
my $new_introns =
find_new_introns( $introns, $hit->{introns} );
push @$introns, map { [@$_] } @$new_introns;
$introns = [ sort { $a->[0] <=> $b->[0] } @$introns ];
}
else {
# initialise the summary feature data
$start = $hit->{features}->[0]->start;
$end = $hit->{features}->[-1]->end;
$score = $hit->{tot_score};
$introns = $hit->{introns};
}
$filtered++;
}
if ( defined $start ) {
# create our summary features with the maximal set of
# introns
for my $intron (@$introns) {
my $summary = Bio::EnsEMBL::SimpleFeature->new(
-start => $start,
-end => $intron->[0],
-strand => $cluster->{strand},
-score => $score,
-display_label =>
sprintf( "summary feature from %d redundant hits",
$filtered ),
-analysis => $self->analysis()
);
push @summary_features, $summary;
$start = $intron->[1];
}
my $summary = Bio::EnsEMBL::SimpleFeature->new(
-start => $start,
-end => $end,
-strand => $cluster->{strand},
-score => $score,
-display_label =>
sprintf( "summary feature from %d redundant hits",
$filtered ),
-analysis => $self->analysis()
);
push @summary_features, $summary;
}
$tot_filtered += $filtered;
}
}
print STDERR
"ClusterDepthFilter: built summary features from $tot_filtered filtered hits\n";
return \@summary_features;
}
sub filter_features {
my ( $self, $meta_clusters, $hits_to_keep, $no_filter, $matching_taxa,
$max_hits_per_meta_cluster )
= @_;
my @retained_features = ();
my @summary_features = ();
my $retained = 0;
for my $meta_cluster (@$meta_clusters) {
my @clusters = @{ $meta_cluster->{clusters} };
for my $cluster (@clusters) {
# sort the hits in this cluster by tot_score, breaking ties
# according to avg_percentid
$cluster->{hits} = [
sort {
( $b->{tot_score} <=> $a->{tot_score} )
|| ( $b->{avg_percentid} <=> $a->{avg_percentid} )
} @{ $cluster->{hits} }
];
# and add the features of the $hits_to_keep best hits to
# the list of filtered features
my $added = 0;
print STDERR "ClusterDepthFilter: adding features of cluster: ",
$cluster->{start}, "-", $cluster->{end}, "\n"
if $DEBUG;
while ( $added < $hits_to_keep && @{ $cluster->{hits} } ) {
my $hit_to_keep = shift @{ $cluster->{hits} };
$added++;
print STDERR "ClusterDepthFilter: adding features of hit: ",
$hit_to_keep->{start}, "-", $hit_to_keep->{end}, "\n"
if $DEBUG;
for my $af ( @{ $hit_to_keep->{features} } ) {
print STDERR "ClusterDepthFilter: adding feature: ",
$af->start, "-", $af->end, "\n"
if $DEBUG;
$af->analysis( $self->analysis );
$af->dbID(0);
$af->{adaptor} = undef;
push @retained_features, $af;
}
}
$meta_cluster->{hits_added} += $added;
}
print STDERR "ClusterDepthFilter: meta-cluster hits added: ".
$meta_cluster->{hits_added}."\n" if $DEBUG;
if ( $no_filter
&& $max_hits_per_meta_cluster
&& ( $meta_cluster->{hits_added} < $max_hits_per_meta_cluster ) )
{
# find candidate hits to retain from hits from matching taxa
my @candidates = ();
for my $cluster (@clusters) {
for my $hit ( @{ $cluster->{hits} } ) {
print STDERR "ClusterDepthFilter: candidate hit taxon_id: ".hit_str($hit)." ".$hit->{taxon_id}."\n" if $DEBUG;
if ( grep { /^$hit->{taxon_id}$/ } @$matching_taxa ) {
push @candidates, $hit;
print STDERR "ClusterDepthFilter: candidate hit: ".hit_str($hit)."\n" if $DEBUG;
}
}
}
# sort these by score & percent_id
@candidates = sort {
( $b->{tot_score} <=> $a->{tot_score} )
|| ( $b->{avg_percentid} <=> $a->{avg_percentid} )
} @candidates;
# and add as many as possible
while ($meta_cluster->{hits_added} < $max_hits_per_meta_cluster
&& @candidates )
{
my $hit_to_keep = shift @candidates;
$meta_cluster->{hits_added}++;
$retained++;
for my $af ( @{ $hit_to_keep->{features} } ) {
print STDERR "ClusterDepthFilter: adding extra feature: ",
$af->start, "-", $af->end, "\n"
if $DEBUG;
$af->analysis( $self->analysis );
$af->dbID(0);
$af->{adaptor} = undef;
push @retained_features, $af;
}
}
}
}
print STDERR
"ClusterDepthFilter: $retained features retained from matching taxa\n";
my $summary_features = $self->build_summary_features($meta_clusters);
return ( \@retained_features, $summary_features );
}
sub _sneaky_new {
my ($class) = @_;
my $self = bless {},$class;
return $self;
}
sub depth_filter {
my $self = shift;
my ( $orig_features, $slice, $max_coverage, $percentid_cutoff,
$hits_to_keep, $no_filter, $max_hits_per_meta_cluster, $hit_db )
= @_;
print STDERR "ClusterDepthFilter: HitsToKeep=$hits_to_keep\n";
print STDERR "ClusterDepthFilter: PercentIdCutoff=$percentid_cutoff\n";
print STDERR "ClusterDepthFilter: NoFilter=$no_filter\n" if $no_filter;
print STDERR
"ClusterDepthFilter: MaxHitsPerMetaCluster=$max_hits_per_meta_cluster\n";
print STDERR "ClusterDepthFilter: "
. scalar(@$orig_features)
. " features before filtering\n";
# features from these taxa should be retained
my @matching_taxa = ();
# (though only fill in this list if we'll actually use it)
if ($no_filter) {
@matching_taxa = @{ $self->get_taxon_id_child($no_filter) };
push @matching_taxa, $no_filter;
}
my $grouped_by_name =
$self->group_features_by_name( $orig_features, $percentid_cutoff,
$no_filter );
print STDERR "ClusterDepthFilter: "
. scalar( keys %$grouped_by_name )
. " unique hitnames\n";
# first break apart any hits that contain discontinuous hits
my $hits =
$self->break_discontinuities( $grouped_by_name, $no_filter, $slice );
if ($SANITY_CHECK_STRANDS) {
for my $hit (@$hits) {
for my $af ( @{ $hit->{features} } ) {
if ( $af->hstrand != $hit->{strand} ) {
my $af_name = $af->hseqname;
die "mismatching strands in hit group '$af_name'\n";
}
}
}
}
print STDERR "ClusterDepthFilter: "
. scalar(@$hits)
. " hits after processing discontinuities\n";
# identify clusters of hits
my $clusters = $self->cluster_hits($hits);
#my $clusters2 = $self->cluster_hits_by_strings($hits);
print STDERR "ClusterDepthFilter: grouped "
. scalar(@$hits)
. " hits into "
. scalar(@$clusters)
. " clusters";
print "\n\n";
#die;
if ($SANITY_CHECK_STRANDS) {
for my $cluster ( @$clusters ) {
for my $hit ( @{ $cluster->{hits} } ) {
for my $af ( @{ $hit->{features} } ) {
if ( $af->hstrand != $cluster->{strand} ) {
die "mismatching strands in clusters\n";
}
}
}
}
}
print STDERR sprintf( " (average of %.2f hits per cluster)",
( scalar(@$hits) / scalar(@$clusters) ) )
if @$clusters > 0;
print STDERR "\n";
map { print STDERR cluster_str($_), "\n" } @$clusters if $DEBUG;
# compute the meta-clusters
my $meta_clusters = $self->cluster_clusters($clusters);
print STDERR "ClusterDepthFilter: grouped "
. scalar(@$clusters)
. " clusters into "
. scalar(@$meta_clusters)
. " meta clusters\n";
if ($SANITY_CHECK_STRANDS) {
for my $meta (@$meta_clusters) {
for my $cluster ( @{ $meta->{clusters} } ) {
for my $hit ( @{ $cluster->{hits} } ) {
for my $af ( @{ $hit->{features} } ) {
if ( $af->hstrand != $meta->{strand} ) {
die "mismatching strands in meta clusters";
}
}
}
}
}
}
# now actually identify the features we want to include
my ( $filtered_features, $summary_features ) =
$self->filter_features( $meta_clusters, $hits_to_keep, $no_filter,
\@matching_taxa, $max_hits_per_meta_cluster );
print STDERR "ClusterDepthFilter: "
. scalar(@$summary_features)
. " summary features\n";
print STDERR "ClusterDepthFilter: "
. scalar(@$filtered_features)
. " features after filtering\n";
return ( $filtered_features, $summary_features );
}
1;
=head1 NAME - Bio::EnsEMBL::Analysis::RunnableDB::Finished::ClusterDepthFilter
=head2 AUTHOR
Graham Ritchie B<email> gr5@sanger.ac.uk
| kiwiroy/ensembl-analysis | modules/Bio/EnsEMBL/Analysis/RunnableDB/Finished/ClusterDepthFilter.pm | Perl | apache-2.0 | 22,419 |
package Paws::DMS::Connection;
use Moose;
has EndpointArn => (is => 'ro', isa => 'Str');
has EndpointIdentifier => (is => 'ro', isa => 'Str');
has LastFailureMessage => (is => 'ro', isa => 'Str');
has ReplicationInstanceArn => (is => 'ro', isa => 'Str');
has ReplicationInstanceIdentifier => (is => 'ro', isa => 'Str');
has Status => (is => 'ro', isa => 'Str');
1;
### main pod documentation begin ###
=head1 NAME
Paws::DMS::Connection
=head1 USAGE
This class represents one of two things:
=head3 Arguments in a call to a service
Use the attributes of this class as arguments to methods. You shouldn't make instances of this class.
Each attribute should be used as a named argument in the calls that expect this type of object.
As an example, if Att1 is expected to be a Paws::DMS::Connection object:
$service_obj->Method(Att1 => { EndpointArn => $value, ..., Status => $value });
=head3 Results returned from an API call
Use accessors for each attribute. If Att1 is expected to be an Paws::DMS::Connection object:
$result = $service_obj->Method(...);
$result->Att1->EndpointArn
=head1 DESCRIPTION
This class has no description
=head1 ATTRIBUTES
=head2 EndpointArn => Str
The Amazon Resource Name (ARN) string that uniquely identifies the
endpoint.
=head2 EndpointIdentifier => Str
The identifier of the endpoint. Identifiers must begin with a letter;
must contain only ASCII letters, digits, and hyphens; and must not end
with a hyphen or contain two consecutive hyphens.
=head2 LastFailureMessage => Str
The error message when the connection last failed.
=head2 ReplicationInstanceArn => Str
The Amazon Resource Name (ARN) of the replication instance.
=head2 ReplicationInstanceIdentifier => Str
The replication instance identifier. This parameter is stored as a
lowercase string.
=head2 Status => Str
The connection status.
=head1 SEE ALSO
This class forms part of L<Paws>, describing an object used in L<Paws::DMS>
=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/DMS/Connection.pm | Perl | apache-2.0 | 2,167 |
# Copyright (c) 2016, Juniper Networks Inc.
# All rights reserved.
#
# 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.
{
'name' => 'BranchLocker',
'domain' => 'example.com',
'word' => 'Default',
#'broadcasts' => [
# 'Some Message.'
#],
# Read only settings, exceptions check for existence of key and not
# the value held in the key.
'readonly' => 0,
'readonly_exceptions' => [
],
'gui_api_key' => 'Super Secret GUI API Key',
'gate_keeper_admin_email' => 'gatekeeper-admin@example.com',
# Branch::Locker config.
'Branch::Locker' => {
'readwrite_user' => 'blr_w',
'readwrite_pass' => '',
'readwrite_host' => 'localhost',
'readonly_user' => 'blr_w',
'readonly_pass' => '',
'databases' => ['branchlocker'],
'database_servers' => {
'local' => ['localhost'],
},
},
'group_order' => [
'Production',
'Service',
'Development',
'Integration',
],
'group_mapping' => {
'Production' => ['Production', 'Feature', 'Release'],
'Service' => ['Service', 'Exception'],
'Development' => ['Development'],
'Integration' => ['Integration'],
},
}
| Juniper/branch-locker | web/BranchLocker/branchlocker.pl | Perl | apache-2.0 | 1,791 |
package VMOMI::CustomFieldDefRemovedEvent;
use parent 'VMOMI::CustomFieldDefEvent';
use strict;
use warnings;
our @class_ancestors = (
'CustomFieldDefEvent',
'CustomFieldEvent',
'Event',
'DynamicData',
);
our @class_members = ( );
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/CustomFieldDefRemovedEvent.pm | Perl | apache-2.0 | 468 |
#!/usr/bin/env perl -w
#---------------------------------------------------------------------------
# Singapore, 21st October 2011
#
# ACADEMIC SOFTWARE LICENSE for TMSOC
# ***********************************
#
# Copyright:
# Wing-Cheong Wong, Sebastian Maurer-Stroh, Georg Schneider, Frank Eisenhaber
# Bioinformatics Institute (BII) A*STAR Singapore
#
# This software is subjected to license restrictions. The software is
# provided as is. In its present form and without written consent of
# the copyright holder, the software is provided in accordance with GPL
# (www.gnu.org/licenses/gpl.html). Among other issues, this excludes any
# warranty and indemnity when using this software. For a commercial license,
# please approach the authors (via email to wongwc@bii.a-star.edu.sg).
#
# When publishing results with this software, please refer to:
# Wing-Cheong Wong, Sebastian Maurer-Stroh, Frank Eisenhaber, 2011,
# "Not all transmembrane helices are born equal: Towards the extension of
# the sequence homology concept to the membrane proteins", Biology Direct
#
# When observing bugs or strange behavior of the software, the user is
# encouraged to contact the authors.
#
#---------------------------------------------------------------------------
#
# This program was modified by Arturo Medrano (UCSD) to take command line
# options and use HHMTOP predicted TMSs, thus removing the need, but keeping
# the option, for the user to provide the TMS.
#
# Date: 11/11/2018
#---------------------------------------------------------------------------
use warnings;
use strict; # Forces variables to be declared
use Data::Dumper;
use Getopt::Long;
use generateTMclassification;
my $i;
my $j;
my $k;
my @tmp1 = ();
my @tmp2 = ();
my @seqname = ();
my @FASTAseq = ();
my @TMsegments = ();
my $sequence = "";
my $segments = "";
my $resultsRef;
my @results;
my $newFASTAseq;
#Variables added by Arturo Medrano
my $seqFile = "";
my $tmsFile = "";
my $outdir = ".";
my $outfile = "";
my $predTMS = 1; #Indicates whether TMS should be predicted by HMMTOP
my $tmsFormat = "HMMTOP";
my $onlyMasked = 0; #Indicates whether only masked sequences will be printed
my %noTMS = ();
#Read command line
read_command_line();
#print Data::Dumper->Dump([$seqFile, $tmsFile, $predTMS, $tmsFormat, $onlyMasked, $outdir, $outfile ],
# [qw(*seqFile *tmsFile *predTMS *tmsFormat *onlyMasked *outdir *outfile)]);
#exit;
#If TMS are going to be predicted, make sure to remove sequences with 0 TMSs, as
#it doesn't make sense to run the program in those sequences.
predictTMS() if ($predTMS);
#Read TMS coordinates
readCVSfileCoords() unless (scalar(@TMsegments) > 0);
#Read FASTA sequences
readSequences();
#Estimate simple and complex TMSs from here
if (scalar(@FASTAseq)==scalar(@TMsegments) && scalar(@FASTAseq)>0) {
my $fh = undef;
if ($outfile) {
open ($fh, ">", $outfile) || die $!;
}
else { $fh = *STDOUT; }
for ($i=0; $i<scalar(@FASTAseq); $i++) {
# Needs to offset the position values by -1; assumes first position starts at 1
@tmp1 = split(/\s+/, $TMsegments[$i]);
my $segment = "";
for ($j=0; $j<scalar(@tmp1); $j++) {
@tmp2 = split(/\,/, $tmp1[$j]);
if ($segment eq "") { $segment = ($tmp2[0]-1).",".($tmp2[1]-1); }
else { $segment = $segment." ".($tmp2[0]-1).",".($tmp2[1]-1); }
}
# Classify the TM region(s)
($resultsRef, $newFASTAseq) = generateTMclassification($segment, $FASTAseq[$i]);
@results = @$resultsRef;
if (uc($FASTAseq[$i]) eq uc($newFASTAseq)) {
$newFASTAseq = "none";
}
# Output the results
if ($onlyMasked) {
print $fh $seqname[$i]."\n".$newFASTAseq."\n\n";
}
else {
print $fh "1. TM segment(s) summary:\n";
for ($j=0; $j<scalar(@results); $j++) {
@tmp1 = split(/\;/,$results[$j]);
print $fh $results[$j]."\n";
}
print $fh "2. Masked FASTA sequence:\n".$seqname[$i]."\n".$newFASTAseq."\n\n";
}
}
}
else {
print "There are ".scalar(@FASTAseq)." sequences but ".scalar(@TMsegments)." associated TM segments. Please check input files(s).\n";
}
###########################################################################
### FUNCTIONS ###
###########################################################################
#==========================================================================
#Read sequence file and avoid sequences without TMSs.
sub readSequences {
my $cnt = 1;
open (my $MYFILE1, "<", $seqFile) || die $!;
while (<$MYFILE1>) {
chomp;
my $line = $_;
$line =~ s/\r//g; # remove linefeed char
$line =~ s/\n//g; # remove new line char
if ($line =~ /^>/) {
if ($sequence ne "") {
push(@FASTAseq, $sequence) unless (exists $noTMS{$cnt});
$sequence = "";
# print "|$cnt|\n", Data::Dumper->Dump([\@seqname, \@FASTAseq, \%noTMS], [qw(*seqname *FASTAseq *noTMS)]);
# <STDIN>;
$cnt++;
}
@tmp1 = split(/\s+/, $line);
push(@seqname, $tmp1[0]) unless (exists $noTMS{$cnt});
}
else { $sequence = $sequence.$line; }
}
close($MYFILE1);
push(@FASTAseq, $sequence) unless (exists $noTMS{$cnt});
# print Data::Dumper->Dump([\@TMsegments, \%noTMS, \@seqname, \@FASTAseq, $cnt], [qw(*TMsegments *noTMS *seqname *FASTAseq *cnt)]);
# exit;
}
#==========================================================================
#Reast TMS coordiantes in CSV format
sub readCVSfileCoords {
# Read TM segments associated to FASTA sequences
open (my $MYFILE2, "<", $tmsFile) || die $!;
while (<$MYFILE2>) {
chomp;
my $line = $_;
$line =~ s/\r//g; # remove linefeed char
$line =~ s/\n//g; # remove new line char
@tmp1 = split(/\s+/, $line);
if (scalar(@tmp1) > 0) {
push(@TMsegments, $line);
}
}
close($MYFILE2);
}
#==========================================================================
#Run HMMTOP on sequences and put them in CSV format for TMSOC
#also remove sequences with 0 TMS, as TMSOC won't run properly on
#Those sequences.
sub predictTMS {
#Generate random integer between 10,0000 and 100,000
my $randNumber = int(rand 90000) + 10000;
#run HMMTOP
my $hmmtopFile = "$outdir/hmmtop_${randNumber}.out";
my $cmd = qq(hmmtop -if=$seqFile -of=$hmmtopFile -sf=FAS -pi=spred -is=pseudo);
system $cmd unless (-f $hmmtopFile && !(-z $hmmtopFile));
#Parse HMMTOP output and get the coordinates in CSV format
open(my $fh, "<", $hmmtopFile) || die $!;
my $cnt = 1;
while(<$fh>) {
chomp;
#Remove trailing white spaces
s/\s+$//;
my $n = undef;
my $tms = undef;
if (/\s+(IN|OUT)\s+(\d+)/) {
$n = $2;
unless ($n == 0) {
if (/(IN|OUT)\s+\d+\s+(.+)$/) {
$tms = $2;
}
}
}
if ($n == 0) { $noTMS{$cnt} = 1; }
else {
die "Error, there should be TMS: n=$n tms=$tms\nline:$_\n" unless ($tms);
#Format the hhmtop coordiantes into CSV coordinates
my $cvs = format_hmmtop2cvs($tms);
die "Could not format hmmtop coords to cvs: $tms" unless ($cvs);
push (@TMsegments, $cvs);
$cnt++;
}
}
close $fh;
system "rm $hmmtopFile" if (-f $hmmtopFile);
}
#==========================================================================
#Format HMMTOP coordinates string to CVS for TMSOC
sub format_hmmtop2cvs {
my $hmmtopStr = shift;
my @tms = split(/\s+/, $hmmtopStr);
my @cvs = ();
for(my $i=0; $i <= $#tms - 1; $i += 2) {
my $left = $tms[$i];
my $right = $tms[$i + 1];
push(@cvs, "${left},${right}");
}
my $str = join("\t", @cvs);
}
#==========================================================================
#Read the command line arguments
sub read_command_line {
print_help() unless (@ARGV);
my $status = GetOptions(
"s|inseqs=s" => \&read_inseqs,
"t|tms=s" => \&read_tms,
"f|tms-format=s" => \&read_tmsFormat,
"p|predict-tms=s" => \&read_predict,
"m|masked-seqs-only=s" => \&read_mask,
"d|outdir=s" => \$outdir,
"o|outfile=s" => \&read_outfile,
"h|help" => sub { print_help(); },
"<>" => sub { die "Error: Unknown argument: $_[0]\n"; });
exit unless ($status);
#If TMSs are given, make sure to avoid running HMMTOP, even if the
#option is explicitly given by the user.
$predTMS = ($tmsFile)? 0 : 1;
#If no output file is given, do not generate output directory because
#output will be sent to STDOUT
if ($outfile) {
system "mkdir -p $outdir" unless (-d $outdir);
#Generate the full path to the outputfile
$outfile = "$outdir/$outfile" if ($outfile);
}
else {
#If there is no outfile, generate an error if the output directory was given.
#There is no point in generating and empty directory if output is going to STDOUT.
if ($outdir ne ".") {
die "Error: if output dir is different from the default, results can't be sent to STDOUT!\n";
}
}
}
#==========================================================================
#Read option -s
sub read_inseqs {
my ($opt, $value) = @_;
die "Error with Option (-$opt): sequence file does not exist or is empty!\n" unless (-f $value && !(-z $value));
$seqFile = $value;
}
#==========================================================================
#Read option -t
sub read_tms {
my ($opt, $value) = @_;
unless (-f $value && !(-z $value)) {
die "Error with option (-$opt): File with TMS does not exist or is empty!";
}
$tmsFile = $value;
}
#==========================================================================
#Read option -f
sub read_tmsFormat {
my ($opt, $value) = @_;
my $tmp = uc($value);
if ($tmp =~ /^(HMMTOP|CSV)$/) {
#If option is HMMTOP, variable just takes the default value
$tmsFormat = $tmp;
}
else {
die "Error with Option (-$opt): valid options are hmmtop|csv!\n";
}
}
#==========================================================================
#Read option -p
sub read_predict {
my ($opt, $value) = @_;
my $tmp = uc($value);
if ($tmp =~ /^[TF]$/) {
#If option is T, variable just takes the default value
$predTMS = 0 if ($tmp eq "F");
}
else {
die "Error: with Option (-$opt): valid options are T|F!\n";
}
}
#==========================================================================
#Read option -m
sub read_mask {
my ($opt, $value) = @_;
my $tmp = uc($value);
if ($tmp =~ /^[TF]$/) {
#If option is F, variable just takes the default value
$onlyMasked = 1 if ($tmp eq "T");
}
else {
die "Error with Option (-$opt): valid options are T|F!";
}
}
#==========================================================================
#Read option -o
sub read_outfile {
my ($opt, $value) = @_;
$outfile = $value;
}
#==========================================================================
#Read option -h
sub print_help {
my $help = <<'HELP';
This program runs the script TMSOC to determine whether TMSs are
simple or complex.
Input parameters:
-s, --inseqs { FILE } (Mandatory)
Input file in FASTA format with all sequences to be analyzed.
-t, --tms { FILE } (Optional; Default: predict with HMMTOP);
Input file with TMS coordinates either in HMMTOP format
or TMSOC format (comma separated pairs). Each line in this
file must have the same order the the sequeces passed through
the -s option.
-f, --tms-format { string } (Optional; Default: hmmtop)
Indicates the format of the input TMS file. Options are
'hmmtop' and 'csv'. Format csv puts cordinates separated
by commas and TMS separated by spaces (e.g.; 3,20 26,42 ...)
-p, --predict-tms { T|F } (Optional; Default: T)
If true (T), run HMMTOP to predic TMSs. This option is forced
to be true (T) if no file with TMSs is provided, or false (F)
if the file with TMSs is provided.
-m, --masked-seqs-only { T|F } (Optional; Default: F)
Indicate whether the output will contain only sequences with
simple TMSs masked.
-d, --outdir { DIR } (Optional; Default: '.')
Output directory where results will be saved. Use this option
only if you are providing an output file name, otherwise
an error will be generated.
-o, --outfile (Optional; Default: STDOUT)
File in the output directory where results will be saved.
If no output file is given, output is sent to standard output.
-h, --help
Display this help. Also displayed if script is run without arguments.
This option takes precedence over any other option.
HELP
print $help;
exit;
}
| SaierLaboratory/TCDBtools | scripts/tmsoc.pl | Perl | bsd-3-clause | 13,144 |
use utf8;
package Netdisco::DB::Result::DevicePortLog;
# Created by DBIx::Class::Schema::Loader
# DO NOT MODIFY THE FIRST PART OF THIS FILE
use strict;
use warnings;
use base 'DBIx::Class::Core';
__PACKAGE__->table("device_port_log");
__PACKAGE__->add_columns(
"id",
{
data_type => "integer",
is_auto_increment => 1,
is_nullable => 0,
sequence => "device_port_log_id_seq",
},
"ip",
{ data_type => "inet", is_nullable => 1 },
"port",
{ data_type => "text", is_nullable => 1 },
"reason",
{ data_type => "text", is_nullable => 1 },
"log",
{ data_type => "text", is_nullable => 1 },
"username",
{ data_type => "text", is_nullable => 1 },
"userip",
{ data_type => "inet", is_nullable => 1 },
"action",
{ data_type => "text", is_nullable => 1 },
"creation",
{
data_type => "timestamp",
default_value => \"current_timestamp",
is_nullable => 1,
original => { default_value => \"now()" },
},
);
# Created by DBIx::Class::Schema::Loader v0.07015 @ 2012-01-07 14:20:02
# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:5moCbYoDG2BqT7VrP/MRkA
# You can replace this text with custom code or comments, and it will be preserved on regeneration
1;
| jeneric/netdisco-frontend-sandpit | Netdisco/lib/Netdisco/DB/Result/DevicePortLog.pm | Perl | bsd-3-clause | 1,243 |
# Functions for collecting general system info
BEGIN { push(@INC, ".."); };
eval "use WebminCore;";
&init_config();
$systeminfo_cron_cmd = "$module_config_directory/systeminfo.pl";
$collected_info_file = "$module_config_directory/info";
$historic_info_dir = "$module_config_directory/history";
# collect_system_info()
# Returns a hash reference containing system information
sub collect_system_info
{
my $info = { };
if (&foreign_check("proc")) {
# CPU and memory
&foreign_require("proc", "proc-lib.pl");
if (defined(&proc::get_cpu_info)) {
my @c = &proc::get_cpu_info();
$info->{'load'} = \@c;
}
my @procs = &proc::list_processes();
$info->{'procs'} = scalar(@procs);
if (defined(&proc::get_memory_info)) {
my @m = &proc::get_memory_info();
$info->{'mem'} = \@m;
if ($m[0] > 128*1024*1024 && $gconfig{'os_type'} eq 'freebsd') {
# Some Webmin versions overstated memory by a factor
# of 1k on FreeBSD - fix it
$m[0] /= 1024;
$m[1] /= 1024;
}
}
# CPU and kernel
my ($r, $m, $o) = &proc::get_kernel_info();
$info->{'kernel'} = { 'version' => $r,
'arch' => $m,
'os' => $o };
}
# Disk space on local filesystems
if (&foreign_check("mount")) {
&foreign_require("mount");
($info->{'disk_total'}, $info->{'disk_free'}) =
&mount::local_disk_space();
}
# Available package updates
if (&foreign_installed("package-updates") && $config{'collect_pkgs'}) {
&foreign_require("package-updates");
my @poss = &package_updates::list_possible_updates(2, 1);
$info->{'poss'} = \@poss;
}
# CPU and drive temps
my @cpu = &get_current_cpu_temps();
$info->{'cputemps'} = \@cpu if (@cpu);
my @drive = &get_current_drive_temps();
$info->{'drivetemps'} = \@drive if (@drive);
# IO input and output
if ($gconfig{'os_type'} =~ /-linux$/) {
local $out = &backquote_command("vmstat 1 2 2>/dev/null");
if (!$?) {
local @lines = split(/\r?\n/, $out);
local @w = split(/\s+/, $lines[$#lines]);
shift(@w) if ($w[0] eq '');
if ($w[8] =~ /^\d+$/ && $w[9] =~ /^\d+$/) {
# Blocks in and out
$info->{'io'} = [ $w[8], $w[9] ];
# CPU user, kernel, idle, io, vm
$info->{'cpu'} = [ @w[12..16] ];
}
}
}
return $info;
}
# get_collected_info()
# Returns the most recently collected system information, or the current info
sub get_collected_info
{
my $infostr = $config{'collect_interval'} eq 'none' ? undef :
&read_file_contents($collected_info_file);
if ($infostr) {
my $info = &unserialise_variable($infostr);
if (ref($info) eq 'HASH' && keys(%$info) > 0) {
return $info;
}
}
return &collect_system_info();
}
# save_collected_info(&info)
# Save information collected on schedule
sub save_collected_info
{
my ($info) = @_;
&open_tempfile(INFO, ">$collected_info_file");
&print_tempfile(INFO, &serialise_variable($info));
&close_tempfile(INFO);
}
# refresh_possible_packages(&newpackages)
# Refresh regularly collected info on available packages
sub refresh_possible_packages
{
my ($pkgs) = @_;
my %pkgs = map { $_, 1 } @$pkgs;
my $info = &get_collected_info();
if ($info->{'poss'} && &foreign_installed("package-updates")) {
&foreign_require("package-updates");
my @poss = &package_updates::list_possible_updates(2);
$info->{'poss'} = \@poss;
}
&save_collected_info($info);
}
# add_historic_collected_info(&info, time)
# Add to the collected info log files the current CPU load, memory uses, swap
# use, disk use and other info we might want to graph
sub add_historic_collected_info
{
my ($info, $time) = @_;
if (!-d $historic_info_dir) {
&make_dir($historic_info_dir, 0700);
}
my @stats;
push(@stats, [ "load", $info->{'load'}->[0] ]) if ($info->{'load'});
push(@stats, [ "load5", $info->{'load'}->[1] ]) if ($info->{'load'});
push(@stats, [ "load15", $info->{'load'}->[2] ]) if ($info->{'load'});
push(@stats, [ "procs", $info->{'procs'} ]) if ($info->{'procs'});
if ($info->{'mem'}) {
push(@stats, [ "memused",
($info->{'mem'}->[0]-$info->{'mem'}->[1])*1024,
$info->{'mem'}->[0]*1024 ]);
if ($info->{'mem'}->[2]) {
push(@stats, [ "swapused",
($info->{'mem'}->[2]-$info->{'mem'}->[3])*1024,
$info->{'mem'}->[2]*1024 ]);
}
}
if ($info->{'disk_total'}) {
push(@stats, [ "diskused",
$info->{'disk_total'}-$info->{'disk_free'},
$info->{'disk_total'} ]);
}
# Get network traffic counts since last run
if (&foreign_check("net") && $gconfig{'os_type'} =~ /-linux$/) {
# Get the current byte count
my $rxtotal = 0;
my $txtotal = 0;
if ($config{'collect_ifaces'}) {
# From module config
@ifaces = split(/\s+/, $config{'collect_ifaces'});
}
else {
# Get list from net module
&foreign_require("net");
foreach my $i (&net::active_interfaces()) {
if ($i->{'virtual'} eq '' &&
$i->{'name'} =~ /^(eth|ppp|wlan|ath|wlan)/) {
push(@ifaces, $i->{'name'});
}
}
}
my $ifaces = join(" ", @ifaces);
foreach my $iname (@ifaces) {
&clean_language();
my $out = &backquote_command(
"ifconfig ".quotemeta($iname)." 2>/dev/null");
&reset_environment();
my $rx = $out =~ /RX\s+bytes:\s*(\d+)/i ? $1 : undef;
my $tx = $out =~ /TX\s+bytes:\s*(\d+)/i ? $1 : undef;
$rxtotal += $rx;
$txtotal += $tx;
}
# Work out the diff since the last run, if we have it
my %netcounts;
if (&read_file("$historic_info_dir/netcounts", \%netcounts) &&
$netcounts{'rx'} && $netcounts{'tx'} &&
$netcounts{'ifaces'} eq $ifaces &&
$rxtotal >= $netcounts{'rx'} && $txtotal >= $netcounts{'tx'}) {
my $secs = ($now - $netcounts{'now'}) * 1.0;
if ($secs) {
my $rxscaled = ($rxtotal - $netcounts{'rx'}) / $secs;
my $txscaled = ($txtotal - $netcounts{'tx'}) / $secs;
if ($rxscaled >= $netcounts{'rx_max'}) {
$netcounts{'rx_max'} = $rxscaled;
}
if ($txscaled >= $netcounts{'tx_max'}) {
$netcounts{'tx_max'} = $txscaled;
}
push(@stats, [ "rx",$rxscaled, $netcounts{'rx_max'} ]);
push(@stats, [ "tx",$txscaled, $netcounts{'tx_max'} ]);
}
}
# Save the last counts
$netcounts{'rx'} = $rxtotal;
$netcounts{'tx'} = $txtotal;
$netcounts{'now'} = $now;
$netcounts{'ifaces'} = $ifaces;
&write_file("$historic_info_dir/netcounts", \%netcounts);
}
# Get drive temperatures
my ($temptotal, $tempcount);
foreach my $t (@{$info->{'drivetemps'}}) {
$temptotal += $t->{'temp'};
$tempcount++;
}
if ($temptotal) {
push(@stats, [ "drivetemp", $temptotal / $tempcount ]);
}
# Get CPU temperature
my ($temptotal, $tempcount);
foreach my $t (@{$info->{'cputemps'}}) {
$temptotal += $t->{'temp'};
$tempcount++;
}
if ($temptotal) {
push(@stats, [ "cputemp", $temptotal / $tempcount ]);
}
# Get IO blocks
if ($info->{'io'}) {
push(@stats, [ "bin", $info->{'io'}->[0] ]);
push(@stats, [ "bout", $info->{'io'}->[1] ]);
}
# Get CPU user and IO time
if ($info->{'cpu'}) {
push(@stats, [ "cpuuser", $info->{'cpu'}->[0] ]);
push(@stats, [ "cpukernel", $info->{'cpu'}->[1] ]);
push(@stats, [ "cpuidle", $info->{'cpu'}->[2] ]);
push(@stats, [ "cpuio", $info->{'cpu'}->[3] ]);
}
# Write to the file
foreach my $stat (@stats) {
open(HISTORY, ">>$historic_info_dir/$stat->[0]");
print HISTORY $time," ",$stat->[1],"\n";
close(HISTORY);
}
# Update the file storing the max possible value for each variable
my %maxpossible;
&read_file("$historic_info_dir/maxes", \%maxpossible);
foreach my $stat (@stats) {
if ($stat->[2] && $stat->[2] > $maxpossible{$stat->[0]}) {
$maxpossible{$stat->[0]} = $stat->[2];
}
}
&write_file("$historic_info_dir/maxes", \%maxpossible);
}
# list_historic_collected_info(stat, [start], [end])
# Returns an array of times and values for some stat, within the given
# time period
sub list_historic_collected_info
{
my ($stat, $start, $end) = @_;
my @rv;
my $last_time;
my $now = time();
open(HISTORY, "$historic_info_dir/$stat");
while(<HISTORY>) {
chop;
my ($time, $value) = split(" ", $_);
next if ($time < $last_time || # No time travel or future data
$time > $now);
if ((!defined($start) || $time >= $start) &&
(!defined($end) || $time <= $end)) {
push(@rv, [ $time, $value ]);
}
if (defined($end) && $time > $end) {
last; # Past the end point
}
$last_time = $time;
}
close(HISTORY);
return @rv;
}
# list_all_historic_collected_info([start], [end])
# Returns a hash mapping stats to data within some time period
sub list_all_historic_collected_info
{
my ($start, $end) = @_;
foreach my $f (&list_historic_stats()) {
my @rv = &list_historic_collected_info($f, $start, $end);
$all{$f} = \@rv;
}
closedir(HISTDIR);
return \%all;
}
# get_historic_maxes()
# Returns a hash reference from stats to the max possible values ever seen
sub get_historic_maxes
{
my %maxpossible;
&read_file("$historic_info_dir/maxes", \%maxpossible);
return \%maxpossible;
}
# get_historic_first_last(stat)
# Returns the Unix time for the first and last stats recorded
sub get_historic_first_last
{
my ($stat) = @_;
open(HISTORY, "$historic_info_dir/$stat") || return (undef, undef);
my $first = <HISTORY>;
$first || return (undef, undef);
chop($first);
my ($firsttime, $firstvalue) = split(" ", $first);
seek(HISTORY, 2, -256) || seek(HISTORY, 0, 0);
while(<HISTORY>) {
$last = $_;
}
close(HISTORY);
chop($last);
my ($lasttime, $lastvalue) = split(" ", $last);
return ($firsttime, $lasttime);
}
# list_historic_stats()
# Returns a list of variables on which we have stats
sub list_historic_stats
{
my @rv;
opendir(HISTDIR, $historic_info_dir);
foreach my $f (readdir(HISTDIR)) {
if ($f =~ /^[a-z]+[0-9]*$/ && $f ne "maxes" && $f ne "procmailpos" &&
$f ne "netcounts") {
push(@rv, $f);
}
}
closedir(HISTDIR);
return @rv;
}
# setup_collectinfo_job()
# Creates or updates the Webmin function cron job, based on the interval
# set in the module config
sub setup_collectinfo_job
{
&foreign_require("webmincron");
my $step = $config{'collect_interval'};
if ($step ne 'none') {
# Setup webmin cron (removing old classic cron job)
$step ||= 5;
my $cron = { 'module' => $module_name,
'func' => 'scheduled_collect_system_info',
'interval' => $step * 60,
};
&webmincron::create_webmin_cron($cron, $systeminfo_cron_cmd);
}
else {
# Delete webmin cron
my $cron = &webmincron::find_webmin_cron($module_name,
'scheduled_collect_system_info');
if ($cron) {
&webmincron::delete_webmin_cron($cron);
}
}
}
# get_current_drive_temps()
# Returns a list of hashes, containing device and temp keys
sub get_current_drive_temps
{
my @rv;
if (!$config{'collect_notemp'} &&
&foreign_installed("smart-status")) {
&foreign_require("smart-status");
foreach my $d (&smart_status::list_smart_disks_partitions()) {
my $st = &smart_status::get_drive_status($d->{'device'}, $d);
foreach my $a (@{$st->{'attribs'}}) {
if ($a->[0] =~ /^Temperature\s+Celsius$/i &&
$a->[1] > 0) {
push(@rv, { 'device' => $d->{'device'},
'temp' => int($a->[1]),
'errors' => $st->{'errors'} });
}
}
}
}
return @rv;
}
# get_current_cpu_temps()
# Returns a list of hashes containing core and temp keys
sub get_current_cpu_temps
{
my @rv;
if (!$config{'collect_notemp'} &&
$gconfig{'os_type'} =~ /-linux$/ && &has_command("sensors")) {
&open_execute_command(SENSORS, "sensors </dev/null 2>/dev/null", 1);
while(<SENSORS>) {
if (/Core\s+(\d+):\s+([\+\-][0-9\.]+)/) {
push(@rv, { 'core' => $1,
'temp' => $2 });
}
elsif (/CPU:\s+([\+\-][0-9\.]+)/) {
push(@rv, { 'core' => 0,
'temp' => $1 });
}
}
close(SENSORS);
}
return @rv;
}
# scheduled_collect_system_info()
# Called by Webmin Cron to collect system info
sub scheduled_collect_system_info
{
my $start = time();
# Make sure we are not already running
if (&test_lock($collected_info_file)) {
print STDERR "scheduled_collect_system_info : Already running\n";
return;
}
# Don't diff collected file
$gconfig{'logfiles'} = 0;
$gconfig{'logfullfiles'} = 0;
$WebminCore::gconfig{'logfiles'} = 0;
$WebminCore::gconfig{'logfullfiles'} = 0;
$no_log_file_changes = 1;
&lock_file($collected_info_file);
$info = &collect_system_info();
if ($info) {
&save_collected_info($info);
&add_historic_collected_info($info, $start);
}
&unlock_file($collected_info_file);
}
1;
| xtso520ok/webmin | system-status/system-status-lib.pl | Perl | bsd-3-clause | 12,145 |
#
# $Id: Compress.pm,v eff9afda3723 2015/01/04 12:34:23 gomor $
#
# file::zip brik
#
package Metabrik::File::Compress;
use strict;
use warnings;
use base qw(Metabrik::Shell::Command);
sub brik_properties {
return {
revision => '$Revision: eff9afda3723 $',
tags => [ qw(unstable compress unzip gunzip uncompress) ],
attributes => {
input => [ qw(file) ],
output => [ qw(file) ],
destdir => [ qw(directory) ],
},
commands => {
unzip => [ qw(input|OPTIONAL destdir|OPTIONAL) ],
gunzip => [ qw(input|OPTIONAL output|OPTIONAL) ],
},
require_binaries => {
'unzip' => [ ],
'gunzip' => [ ],
},
};
}
sub brik_use_properties {
my $self = shift;
return {
attributes_default => {
destdir => $self->global->datadir,
},
};
}
sub unzip {
my $self = shift;
my ($input, $destdir) = @_;
$input ||= $self->input;
if (! defined($input)) {
return $self->log->error($self->brik_help_set('input'));
}
$destdir ||= $self->destdir;
if (! defined($destdir)) {
return $self->log->error($self->brik_help_set('destdir'));
}
my $cmd = "unzip -o $input -d $destdir/";
return $self->system($cmd);
}
sub gunzip {
my $self = shift;
my ($input, $output) = @_;
$input ||= $self->input;
if (! defined($input)) {
return $self->log->error($self->brik_help_set('input'));
}
my $file_out;
if (defined($output)) {
$file_out = $output;
}
else {
($file_out = $input) =~ s/.gz$//;
}
my $cmd = "gunzip -c $input > $file_out";
return $self->system($cmd);
}
1;
__END__
=head1 NAME
Metabrik::File::Compress - file::compress Brik
=head1 COPYRIGHT AND LICENSE
Copyright (c) 2014-2015, Patrice E<lt>GomoRE<gt> Auffret
You may distribute this module under the terms of The BSD 3-Clause License.
See LICENSE file in the source distribution archive.
=head1 AUTHOR
Patrice E<lt>GomoRE<gt> Auffret
=cut
| gitpan/Metabrik-Repository | lib/Metabrik/File/Compress.pm | Perl | bsd-3-clause | 2,013 |
#!/usr/bin/perl
use strict;
use warnings;
use WWW::Curl::Easy;
use DBI;
use POSIX qw/strftime/;
use Time::HiRes qw(usleep nanosleep);
my $logFile = "/var/log/srd/scrapeConEd.log";
open LOGFILE, ">>", $logFile or die "Couldnt Open LogFile!\n".$!;
my $configfile = "scrapeConEd.config";
open CONFIGFILE, "+<", $configfile or die "NEED TO CONFIGURE scrapeConEd.config!\n".$!;
my $dbh;
my $group_id;
my @conedArr;
my $last_data_timestamp;
my $current_data_timestamp;
print LOGFILE "Starting scrapeConEd @ ".localtime."\n";
while( my $line = <CONFIGFILE> ) {
if( $line =~ /GROUP_ID=(\d+)/ ) {
$group_id = $1;
} elsif( $line =~ /LAST_DATA_TIMESTAMP=(\w+)/ ) {
$last_data_timestamp = $1;
}
}
if( ! defined($group_id) ) {
print LOGFILE "NEED TO SET : GROUP_ID=#### IN CONFIG FILE!\n";
exit(-1);
} else {
print LOGFILE "GROUP_ID = $group_id \n";
}
if( ! defined($last_data_timestamp) ) {
print LOGFILE "NO EXISTING LAST_DATA_TIMESTAMP FOUND!\n";
} else {
print LOGFILE "LAST_DATA_TIMESTAMP = $last_data_timestamp \n";
}
#my $curlResults = `curl -f http://apps.coned.com/stormcenter_external/stormcenter_externaldata/data/interval_generation_data/metadata.xml?timestamp=00000001 `
#print "TEST=".$curlResults."=TEST\n";
my $curl = WWW::Curl::Easy->new;
$curl->setopt(CURLOPT_HEADER,1);
$curl->setopt(CURLOPT_URL, 'http://apps.coned.com/stormcenter_external/stormcenter_externaldata/data/interval_generation_data/metadata.xml?timestamp=00000001');
# A filehandle, reference to a scalar or reference to a typeglob can be used here.
my $response_body;
$curl->setopt(CURLOPT_WRITEDATA,\$response_body);
# Starts the actual request
my $retcode = $curl->perform;
# Looking at the results...
if ($retcode == 0) {
print LOGFILE "Transfer went ok\n";
if( $response_body =~ /<directory>(\w+)<\/directory>/ ) {
$current_data_timestamp = $1;
seek(CONFIGFILE, 0, 0) or die "can't seek to start of $configfile: $!";
print CONFIGFILE "#scrapeConEd CONFIG FILE\n" or die "can't print to $configfile: $!";
print CONFIGFILE "GROUP_ID=$group_id\n" or die "can't print to $configfile: $!";
print CONFIGFILE "LAST_DATA_TIMESTAMP=$current_data_timestamp\n" or die "can't print to $configfile: $!";
truncate(CONFIGFILE, tell(CONFIGFILE)) or die "can't truncate $configfile: $!";
print LOGFILE "CURRENT_DATA_TIMESTAMP = $current_data_timestamp\n";
}
}
close(CONFIGFILE);
if( !defined($current_data_timestamp) ) {
print LOGFILE "ERROR: COULD NOT FIND CURRENT_DATA_TIMESTAMP!\n";
exit(-2);
}
if( defined($last_data_timestamp) && $current_data_timestamp eq $last_data_timestamp ) {
print LOGFILE "TIMESTAMP HAS NOT CHANGED SINCE LAST RUN! TIMESTAMP=$last_data_timestamp\n";
exit(-3);
}
my $currentDataTimeDB;
if( $current_data_timestamp =~ /(\d\d\d\d)_(\d\d)_(\d\d)_(\d\d)_(\d\d)_(\d\d)/ ) {
$currentDataTimeDB = "$1-$2-$3 $4:$5:$6";
} else {
print LOGFILE "ERROR: COULD NOT FORMAT TIMESTAMP STRING: $current_data_timestamp\n";
exit(-4);
}
### WE'VE GOT NEW DATA, CLOSE THE EVENTS THAT ARE ALREADY IN THE DB AND THEN GET AND LOAD
### THE NEW DATA.
# connect to database
$dbh = DBI->connect("DBI:Pg:dbname=sitrep;host=localhost", "sitrepadmin", "", {'RaiseError' => 1});
####### NOW PROCESS EACH URL from coned_url_list with current_data_timestamp ###
my @urls;
my $urlfile = "coned_url_list.txt";
open URLFILE, "<", $urlfile or die "NEED TO SUPPLY URL FILE: $urlfile!\n".$!;
while( my $line = <URLFILE> ) {
$line =~ s/REPLACE_STR_HERE/$current_data_timestamp/g;
chomp $line;
push (@urls, $line);
}
#my @urls = <coned_url_list.txt>;
my $lineCount = 0;
foreach my $url (@urls) {
$lineCount++;
if($lineCount % 100 == 0) {
print LOGFILE "PROGRESS AT:".localtime." RETRIEVING URL # $lineCount of ".scalar (@urls)."\n";
print LOGFILE "URL:".$url."\n";
}
$curl->setopt(CURLOPT_URL, $url);
$curl->setopt(CURLOPT_FAILONERROR,1);
my $response_body = "";
$curl->setopt(CURLOPT_WRITEDATA,\$response_body);
my $retcode = $curl->perform;
# print LOGFILE "RETCODE====$retcode\n";
# print LOGFILE "TEST=$response_body";
# Looking at the results...
if ($retcode == 0) {
print LOGFILE "Transfer of url went ok! URL= $url\n";
# print LOGFILE "TEST=$response_body";
# push @conedArr, [$1, $2, $3, $4, $5] while $response_body =~ /"cust_a":"(\d+)","etr":"([^"]+)","cause":"([^"]+)"\}\],"geom":\[\{"p":\[([^,]+),([^\]]+)\]/g;
push @conedArr, [$1, $2, $3, $4, $5, $url] while $response_body =~ /"cust_a":"(\d+)","etr":"([^"]+)","cause":"([^"]+)"\}\],"geom":\[\{"p":\[([^,]+),([^\]]+)\]/g;
}
# while( my $line = <INFILE>) {
## push @conedArr, [$1, $2, $3, $4, $5] while $line =~ /"cust_a":"(\d+)","etr":"([^"]+)","cause":"([^"]+)"\}\],"geom":\[\{"p":\[(\d+),(\d+)\]/g;
# push @conedArr, [$1, $2, $3, $4, $5] while $line =~ /"cust_a":"(\d+)","etr":"([^"]+)","cause":"([^"]+)"\}\],"geom":\[\{"p":\[([^,]+),([^\]]+)\]/g;
# }
# close INFILE;
usleep(200000);
}
#UPDATE ALL ROWS FOR GROUP_ID THAT feature_end=NULL
#my $updateStr = "UPDATE event SET data_end='$currentDataTimeDB' WHERE group_id=$group_id AND has_end=false";
my $updateStr = "UPDATE event SET data_end='$currentDataTimeDB' WHERE group_id=$group_id AND has_end=false";
#print "TEST=$updateStr\n";
my $rows = $dbh->do($updateStr);
print LOGFILE "Customers Affected\tEstimated Time of Restoration\tCause of Outage\tLat\tLon\n";
foreach my $matchArr (@conedArr) {
print LOGFILE ${$matchArr}[0]."\t".${$matchArr}[1]."\t".${$matchArr}[2] ."\t".${$matchArr}[3] ."\t".${$matchArr}[4]." URL=".${$matchArr}[5]."\n";
#INSERT EACH ROW INTO location
my $insertStr = "INSERT INTO location (source, geometry) VALUES ( 7, ST_SetSRID(ST_MakePoint(".${$matchArr}[4].",".${$matchArr}[3].",0),4326) ) RETURNING id";
# my $rows = $dbh->do($insertStr);
my $insert_handle = $dbh->prepare($insertStr);
$insert_handle->execute();
my $locid = $insert_handle->fetch()->[0];
$insert_handle->finish();
#INSERT EACH ROW INTO event
$insertStr = "INSERT INTO event (group_id, data, data_begin, location) VALUES ( $group_id, '\"CustomersAffected\"=>".${$matchArr}[0].", \"EstTimeOfRest\"=>\"".${$matchArr}[1]."\", \"CauseOfOutage\" =>\"".${$matchArr}[2]."\"'::hstore, '$currentDataTimeDB', $locid )";
#print LOGFILE "INSERT_STMT=$insertStr\n";
my $rows = $dbh->do($insertStr);
}
close(LOGFILE);
# Clean up
$dbh->disconnect();
exit(0);
| OSrce/PowerOutageWebScrape | scrapeConEd.pl | Perl | bsd-3-clause | 6,391 |
<?php
$CANT_REDIRECT_IN = 'Nie możesz przekierować zapytania w tym momencie.';
$REDIRECT_ALLOW_ONLY_IN = 'Nie możesz wykonać przekierowania w bloku <b>%s</b>. Wpłynąć na zapytanie możesz jedynie w <b>code.action</b> lub <b>code.ajax</b>.';
$SORRY_CANT_REDIRECT_HERE = 'Nie możesz tutaj przekierować zapytania.'; | charJKL/deArcane | src/Core/_Exception/Runtime/CantRedirectHere.lang.pl | Perl | mit | 321 |
#!/usr/bin/perl
##
## Plots energy levels using GetEnLevels.sh
##
sub print_help(){
print "Usage: ";
print "$0 -f file --N0=N0 --Nf=Nf (--plot --Nlevels=Nlevels --spec) \n";
print " --spec : Generates an additional file with the output of GetEnLevels.sh for each N \n";
exit(0);
}
##
## main
##
use Getopt::Long;
if ( @ARGV > 0 ){
GetOptions('f|file=s'=>\$FileName,
'N0=i' =>\$N0,
'Nf=i' =>\$Nf,
'plot' =>\$plot,
'Nlevels=i'=>\$NlevelsMax,
'spec'=>\$GenSpec,
'h|help' =>\$help);
if (!defined($N0)||!defined($Nf)){print_help();}
if (!$FileName){$FileName="output.txt";}
if (!$NlevelsMax){$NlevelsMax=50;}
}
else{print_help();}
if ($help){print_help();}
print "File = $FileName \n";
print "N0 = $N0 \n";
print "Nf = $Nf \n";
##
## Get energy levels from GetEnLevels.sh
##
my @En_N=(); #List of lists
my $NumNs=0;
##my $NlevelsMax=50;
for ($Ns=$N0;$Ns<=$Nf;$Ns+=2){
my @EnLevels=();
my $nlevels=0;
push(@EnLevels,$Ns); ## set Ns
## $GetEnCommand="GetEnLevels -f $FileName -N $Ns | awk \'{print \$1}\'";
$GetEnCommand="GetEnLevels.sh -f $FileName -N $Ns | awk \'{print \$1}\'";
## print "Command = $GetEnCommand \n";
open (GREPDATA,"$GetEnCommand |");
while (<GREPDATA>){
$TheLine=$_;
chomp($TheLine);
if ($nlevels<=$NlevelsMax){push(@EnLevels,$TheLine);}
$nlevels++;
}
close(GREPDATA);
push(@En_N,\@EnLevels);
print "Obtaining levels: N = $Ns ; ";
print "Nlevels = ".$nlevels." \n";
$NumNs++;
}
##end Loop in Ns
##for ($ii=0;$ii<$NumNs;$ii++){
## print "N = $En_N[$ii][0] En_N = $En_N[$ii][1] $En_N[$ii][2] $En_N[$ii][50]\n";
##}
##
## Constructing the data file
##
open (OUTPUTFILE,"> En_vs_N.dat");
for ($ilev=1;$ilev<=$NlevelsMax;$ilev++){
for ($ii=0;$ii<$NumNs;$ii++){
print OUTPUTFILE "$En_N[$ii][0] $En_N[$ii][$ilev]\n";
}
for ($ii=$NumNs-2;$ii>=0;$ii--){
print OUTPUTFILE "$En_N[$ii][0] $En_N[$ii][$ilev]\n";
}
}
## Loop in levels
close(OUTPUTFILE);
##
## Generate gnuplot
##
if ($plot){
print "Plotting... \n";
open (GPLOT,"| gnuplot -persist") or die "No Gnuplot here \n";
$GnuPlotCommand.="set ylabel \"Levels\" \n set xlabel \"N\" \n";
$GnuPlotCommand.="set xrange[$N0:*] \n";
$GnuPlotCommand.="plot \"En_vs_N.dat\" with lp \n";
print GPLOT $GnuPlotCommand;
close(GPLOT);
print "... done.\n";
} # end if plot
if (defined($GenSpec)){
print "Creating EnLevels.dat ... \n";
open (OUTPUTFILE,"> EnLevels.dat");
for ($Ns=$N0;$Ns<=$Nf;$Ns+=2){
$RawGetEnCommand="GetEnLevels.sh -f $FileName -N $Ns ";
open (GREPDATA,"$RawGetEnCommand |");
while (<GREPDATA>){
$TheLine=$_;
chomp($TheLine);
print OUTPUTFILE "$TheLine \n";
}
close(GREPDATA);
} # end for
close(OUTPUTFILE);
print "... done creating EnLevels.dat \n";
} # end if spec
| cifu9502/nrgcode | src/Scripts/PlotEnLevels.perl | Perl | mit | 2,823 |
package Paws::Pinpoint::UpdateApnsChannelResponse;
use Moose;
has APNSChannelResponse => (is => 'ro', isa => 'Paws::Pinpoint::APNSChannelResponse', required => 1);
use MooseX::ClassAttribute;
class_has _stream_param => (is => 'ro', default => 'APNSChannelResponse');
has _request_id => (is => 'ro', isa => 'Str');
1;
### main pod documentation begin ###
=head1 NAME
Paws::Pinpoint::UpdateApnsChannelResponse
=head1 ATTRIBUTES
=head2 B<REQUIRED> APNSChannelResponse => L<Paws::Pinpoint::APNSChannelResponse>
=head2 _request_id => Str
=cut
| ioanrogers/aws-sdk-perl | auto-lib/Paws/Pinpoint/UpdateApnsChannelResponse.pm | Perl | apache-2.0 | 562 |
package Paws::DynamoDBStreams::DescribeStreamOutput;
use Moose;
has StreamDescription => (is => 'ro', isa => 'Paws::DynamoDBStreams::StreamDescription');
has _request_id => (is => 'ro', isa => 'Str');
### main pod documentation begin ###
=head1 NAME
Paws::DynamoDBStreams::DescribeStreamOutput
=head1 ATTRIBUTES
=head2 StreamDescription => L<Paws::DynamoDBStreams::StreamDescription>
A complete description of the stream, including its creation date and
time, the DynamoDB table associated with the stream, the shard IDs
within the stream, and the beginning and ending sequence numbers of
stream records within the shards.
=head2 _request_id => Str
=cut
1; | ioanrogers/aws-sdk-perl | auto-lib/Paws/DynamoDBStreams/DescribeStreamOutput.pm | Perl | apache-2.0 | 676 |
#------------------------------------------------------------------------------
# File: AFCP.pm
#
# Description: Read/write AFCP trailer
#
# Revisions: 12/26/2005 - P. Harvey Created
#
# References: 1) http://web.archive.org/web/20080828211305/http://www.tocarte.com/media/axs_afcp_spec.pdf
#------------------------------------------------------------------------------
package Image::ExifTool::AFCP;
use strict;
use vars qw($VERSION);
use Image::ExifTool qw(:DataAccess :Utils);
$VERSION = '1.06';
sub ProcessAFCP($$);
%Image::ExifTool::AFCP::Main = (
PROCESS_PROC => \&ProcessAFCP,
NOTES => q{
AFCP stands for AXS File Concatenation Protocol, and is a poorly designed
protocol for appending information to the end of files. This can be used as
an auxiliary technique to store IPTC information in images, but is
incompatible with some file formats.
ExifTool will read and write (but not create) AFCP IPTC information in JPEG
and TIFF images.
See
L<http://web.archive.org/web/20080828211305/http://www.tocarte.com/media/axs_afcp_spec.pdf>
for the AFCP specification.
},
IPTC => { SubDirectory => { TagTable => 'Image::ExifTool::IPTC::Main' } },
TEXT => 'Text',
Nail => {
Name => 'ThumbnailImage',
# (the specification allows for a variable amount of padding before
# the image after a 10-byte header, so look for the JPEG SOI marker,
# otherwise assume a fixed 8 bytes of padding)
RawConv => q{
pos($val) = 10;
my $start = ($val =~ /\xff\xd8\xff/g) ? pos($val) - 3 : 18;
my $img = substr($val, $start);
return $self->ValidateImage(\$img, $tag);
},
},
PrVw => {
Name => 'PreviewImage',
RawConv => q{
pos($val) = 10;
my $start = ($val =~ /\xff\xd8\xff/g) ? pos($val) - 3 : 18;
my $img = substr($val, $start);
return $self->ValidateImage(\$img, $tag);
},
},
);
#------------------------------------------------------------------------------
# Read/write AFCP information in a file
# Inputs: 0) ExifTool object reference, 1) dirInfo reference
# (Set 'ScanForAFCP' member in dirInfo to scan from current position for AFCP)
# Returns: 1 on success, 0 if this file didn't contain AFCP information
# -1 on write error or if the offsets were incorrect on reading
# - updates DataPos to point to actual AFCP start if ScanForAFCP is set
# - updates DirLen to trailer length
# - returns Fixup reference in dirInfo hash when writing
sub ProcessAFCP($$)
{
my ($et, $dirInfo) = @_;
my $raf = $$dirInfo{RAF};
my $curPos = $raf->Tell();
my $offset = $$dirInfo{Offset} || 0; # offset from end of file
my $rtnVal = 0;
NoAFCP: for (;;) {
my ($buff, $fix, $dirBuff, $valBuff, $fixup, $vers);
# look for AXS trailer
last unless $raf->Seek(-12-$offset, 2) and
$raf->Read($buff, 12) == 12 and
$buff =~ /^(AXS(!|\*))/;
my $endPos = $raf->Tell();
my $hdr = $1;
SetByteOrder($2 eq '!' ? 'MM' : 'II');
my $startPos = Get32u(\$buff, 4);
if ($raf->Seek($startPos, 0) and $raf->Read($buff, 12) == 12 and $buff =~ /^$hdr/) {
$fix = 0;
} else {
$rtnVal = -1;
# look for start of AXS trailer if 'ScanForAFCP'
last unless $$dirInfo{ScanForAFCP} and $raf->Seek($curPos, 0);
my $actualPos = $curPos;
# first look for header right at current position
for (;;) {
last if $raf->Read($buff, 12) == 12 and $buff =~ /^$hdr/;
last NoAFCP if $actualPos != $curPos;
# scan for AXS header (could be after preview image)
for (;;) {
my $buf2;
$raf->Read($buf2, 65536) or last NoAFCP;
$buff .= $buf2;
if ($buff =~ /$hdr/g) {
$actualPos += pos($buff) - length($hdr);
last; # ok, now go back and re-read header
}
$buf2 = substr($buf2, -3); # only need last 3 bytes for next test
$actualPos += length($buff) - length($buf2);
$buff = $buf2;
}
last unless $raf->Seek($actualPos, 0); # seek to start of AFCP
}
# calculate shift for fixing AFCP offsets
$fix = $actualPos - $startPos;
}
# set variables returned in dirInfo hash
$$dirInfo{DataPos} = $startPos + $fix; # actual start position
$$dirInfo{DirLen} = $endPos - ($startPos + $fix);
$rtnVal = 1;
my $verbose = $et->Options('Verbose');
my $out = $et->Options('TextOut');
my $outfile = $$dirInfo{OutFile};
if ($outfile) {
# allow all AFCP information to be deleted
if ($$et{DEL_GROUP}{AFCP}) {
$verbose and print $out " Deleting AFCP\n";
++$$et{CHANGED};
last;
}
$dirBuff = $valBuff = '';
require Image::ExifTool::Fixup;
$fixup = $$dirInfo{Fixup};
$fixup or $fixup = $$dirInfo{Fixup} = new Image::ExifTool::Fixup;
$vers = substr($buff, 4, 2); # get version number
} else {
$et->DumpTrailer($dirInfo) if $verbose or $$et{HTML_DUMP};
}
# read AFCP directory data
my $numEntries = Get16u(\$buff, 6);
my $dir;
unless ($raf->Read($dir, 12 * $numEntries) == 12 * $numEntries) {
$et->Error('Error reading AFCP directory', 1);
last;
}
if ($verbose > 2 and not $outfile) {
my $dat = $buff . $dir;
print $out " AFCP Directory:\n";
Image::ExifTool::HexDump(\$dat, undef,
Addr => $$dirInfo{DataPos},
Width => 12,
Prefix => $$et{INDENT},
Out => $out,
);
}
$fix and $et->Warn("Adjusted AFCP offsets by $fix", 1);
#
# process AFCP directory
#
my $tagTablePtr = GetTagTable('Image::ExifTool::AFCP::Main');
my ($index, $entry);
for ($index=0; $index<$numEntries; ++$index) {
my $entry = 12 * $index;
my $tag = substr($dir, $entry, 4);
my $size = Get32u(\$dir, $entry + 4);
my $offset = Get32u(\$dir, $entry + 8);
if ($size < 0x80000000 and
$raf->Seek($offset+$fix, 0) and
$raf->Read($buff, $size) == $size)
{
if ($outfile) {
# rewrite this information
my $tagInfo = $et->GetTagInfo($tagTablePtr, $tag);
if ($tagInfo and $$tagInfo{SubDirectory}) {
my %subdirInfo = (
DataPt => \$buff,
DirStart => 0,
DirLen => $size,
DataPos => $offset + $fix,
Parent => 'AFCP',
);
my $subTable = GetTagTable($tagInfo->{SubDirectory}->{TagTable});
my $newDir = $et->WriteDirectory(\%subdirInfo, $subTable);
if (defined $newDir) {
$size = length $newDir;
$buff = $newDir;
}
}
$fixup->AddFixup(length($dirBuff) + 8);
$dirBuff .= $tag . Set32u($size) . Set32u(length $valBuff);
$valBuff .= $buff;
} else {
# extract information
$et->HandleTag($tagTablePtr, $tag, $buff,
DataPt => \$buff,
Size => $size,
Index => $index,
DataPos => $offset + $fix,
);
}
} else {
$et->Warn("Bad AFCP directory");
$rtnVal = -1 if $outfile;
last;
}
}
if ($outfile and length($dirBuff)) {
my $outPos = Tell($outfile); # get current outfile position
# apply fixup to directory pointers
my $valPos = $outPos + 12; # start of value data
$fixup->{Shift} += $valPos + length($dirBuff);
$fixup->ApplyFixup(\$dirBuff);
# write the AFCP header, directory, value data and EOF record (with zero checksums)
Write($outfile, $hdr, $vers, Set16u(length($dirBuff)/12), Set32u(0),
$dirBuff, $valBuff, $hdr, Set32u($outPos), Set32u(0)) or $rtnVal = -1;
# complete fixup so the calling routine can apply further shifts
$fixup->AddFixup(length($dirBuff) + length($valBuff) + 4);
$fixup->{Start} += $valPos;
$fixup->{Shift} -= $valPos;
}
last;
}
return $rtnVal;
}
1; # end
__END__
=head1 NAME
Image::ExifTool::AFCP - Read/write AFCP trailer
=head1 SYNOPSIS
This module is used by Image::ExifTool
=head1 DESCRIPTION
This module contains definitions required by Image::ExifTool to extract
information from the AFCP trailer. Although the AFCP specification is
compatible with various file formats, ExifTool currently only processes AFCP
in JPEG images.
=head1 NOTES
AFCP is a specification which allows meta information (including IPTC) to be
appended to the end of a file.
It is a poorly designed protocol because (like TIFF) it uses absolute
offsets to specify data locations. This is a huge blunder because it makes
the AFCP information dependent on the file length, so it is easily
invalidated by image editing software which doesn't recognize the AFCP
trailer to fix up these offsets when the file length changes. ExifTool will
attempt to fix these invalid offsets if possible.
Scanning for AFCP information may be time consuming, especially when reading
from a sequential device, since the information is at the end of the file.
In these instances, the ExifTool FastScan option may be used to disable
scanning for AFCP information.
=head1 AUTHOR
Copyright 2003-2014, Phil Harvey (phil at owl.phy.queensu.ca)
This library is free software; you can redistribute it and/or modify it
under the same terms as Perl itself.
=head1 REFERENCES
=over 4
=item L<http://www.tocarte.com/media/axs_afcp_spec.pdf>
=back
=head1 SEE ALSO
L<Image::ExifTool::TagNames/AFCP Tags>,
L<Image::ExifTool(3pm)|Image::ExifTool>
=cut
| pericles-project/pet | nativeTools/exiftool_OSX/lib/Image/ExifTool/AFCP.pm | Perl | apache-2.0 | 10,690 |
# please insert nothing before this line: -*- mode: cperl; cperl-indent-level: 4; cperl-continued-statement-offset: 4; indent-tabs-mode: nil -*-
package TestProtocol::echo_block;
# this test reads from/writes to the socket doing blocking IO
#
# see TestProtocol::echo_timeout for how to do the same with
# nonblocking IO but using the timeout
use strict;
use warnings FATAL => 'all';
use Apache2::Connection ();
use APR::Socket ();
use TestCommon::Utils;
use Apache2::Const -compile => 'OK';
use APR::Const -compile => qw(SO_NONBLOCK);
use constant BUFF_LEN => 1024;
sub handler {
my Apache2::Connection $c = shift;
my APR::Socket $socket = $c->client_socket;
# starting from Apache 2.0.49 several platforms require you to set
# the socket to a blocking IO mode
my $nonblocking = $socket->opt_get(APR::Const::SO_NONBLOCK);
if ($nonblocking) {
$socket->opt_set(APR::Const::SO_NONBLOCK, 0);
# test that we really *are* in the blocking mode
!$socket->opt_get(APR::Const::SO_NONBLOCK)
or die "failed to set blocking mode";
}
while ($socket->recv(my $buffer, BUFF_LEN)) {
die "recv() has returned untainted data:"
unless TestCommon::Utils::is_tainted($buffer);
$socket->send($buffer);
}
Apache2::Const::OK;
}
1;
| dreamhost/dpkg-ndn-perl-mod-perl | t/protocol/TestProtocol/echo_block.pm | Perl | apache-2.0 | 1,328 |
# Functions for editing /etc/mailcap
BEGIN { push(@INC, ".."); };
use WebminCore;
&init_config();
if ($module_info{'usermin'}) {
&switch_to_remote_user();
$mailcap_file = $userconfig{'mailcap'};
if ($mailcap_file !~ /^\//) {
$mailcap_file = "$remote_user_info[7]/$mailcap_file";
}
}
else {
$mailcap_file = $config{'mailcap'};
}
# list_mailcap()
# Returns a list of /etc/mailcap entries
sub list_mailcap
{
if (!scalar(@list_mailcap_cache)) {
@list_mailcap_cache = ( );
open(CAP, $mailcap_file);
local $lnum = 0;
while(<CAP>) {
local ($slnum, $elnum) = ($lnum, $lnum);
s/\r|\n//g;
while (/^(.*)\\/) {
# Continuation line! Read the next one and append it
local $before = $1;
local $nxt = <CAP>;
$nxt =~ s/\r|\n//g;
$_ = $before.$nxt;
$elnum++;
}
if (/^(#*)\s*([a-z0-9\-]+)\/([a-z0-9\-\*]+);\s*([^;]*)(;(.*))?/) {
# Found a line
local @cmtlines = split(/\n/, $cmt);
local $cap = { 'type' => $2."/".$3,
'program' => $4,
'enabled' => !$1,
'cmt' => $cmt,
'args' => { },
'line' => $slnum-scalar(@cmtlines),
'eline' => $elnum,
'index' => scalar(@list_mailcap_cache),
};
# Parse ; separated args after the command
local $args = $6;
local @args = split(/\s*;\s*/, $args);
foreach my $arg (@args) {
if ($arg =~ /^\s*(\S+)\s*=\s*(.*)/) {
# A name-value arg
$cap->{'args'}->{$1} = $2;
}
elsif ($arg =~ /^\s*(\S+)\s*$/) {
$cap->{'args'}->{$1} = "";
}
}
push(@list_mailcap_cache, $cap);
$cmt = undef;
}
elsif (/^#+(.*)/) {
# Found a comment before a rule
if ($cmt) {
$cmt .= "\n".$1;
}
else {
$cmt = $1;
}
}
else {
$cmt = undef;
}
$lnum++;
}
close(CAP);
}
return @list_mailcap_cache;
}
# create_mailcap(&mailcap)
# Adds a mailcap entry
sub create_mailcap
{
local ($mailcap) = @_;
&list_mailcap(); # init cache
local $lref = &read_file_lines($mailcap_file);
local @lines = &mailcap_lines($mailcap);
$mailcap->{'line'} = scalar(@$lref);
$mailcap->{'eline'} = scalar(@$lref)+scalar(@lines)-1;
$mailcap->{'index'} = scalar(@list_mailcap_cache);
push(@$lref, @lines);
&flush_file_lines($mailcap_file);
push(@list_mailcap_cache, $mailcap);
}
# modify_mailcap(&mailcap)
# Updates one mailcap entry in the file
sub modify_mailcap
{
local ($mailcap) = @_;
local $lref = &read_file_lines($mailcap_file);
local @lines = &mailcap_lines($mailcap);
local $oldlen = $mailcap->{'eline'} - $mailcap->{'line'} + 1;
splice(@$lref, $mailcap->{'line'}, $oldlen, @lines);
&flush_file_lines($mailcap_file);
local $diff = scalar(@lines)-$oldlen;
foreach my $c (grep { $c ne $mailcap } @list_mailcap_cache) {
$c->{'line'} += $diff if ($c->{'line'} > $mailcap->{'line'});
$c->{'eline'} += $diff if ($c->{'eline'} > $mailcap->{'line'});
}
}
# delete_mailcap(&mailcap)
# Removes one mailcap entry from the file
sub delete_mailcap
{
local ($mailcap) = @_;
local $lref = &read_file_lines($mailcap_file);
local $len = $mailcap->{'eline'} - $mailcap->{'line'} + 1;
splice(@$lref, $mailcap->{'line'}, $len);
&flush_file_lines($mailcap_file);
@list_mailcap_cache = grep { $_ ne $mailcap } @list_mailcap_cache;
foreach my $c (@list_mailcap_cache) {
$c->{'line'} -= $len if ($c->{'line'} > $mailcap->{'line'});
$c->{'eline'} -= $len if ($c->{'eline'} > $mailcap->{'line'});
$c->{'index'}-- if ($c->{'index'} > $mailcap->{'index'});
}
}
# mailcap_lines(&mailcap)
# Returns an array of lines for a mailcap entry
sub mailcap_lines
{
local ($mailcap) = @_;
local @rv;
local $args;
foreach my $a (keys %{$mailcap->{'args'}}) {
local $v = $mailcap->{'args'}->{$a};
if ($v eq '') {
$args .= "; $a";
}
else {
$args .= "; $a=$v";
}
}
foreach my $l (split(/\n/, $mailcap->{'cmt'})) {
push(@rv, "#$l");
}
push(@rv, ($mailcap->{'enabled'} ? "" : "#").
"$mailcap->{'type'}; $mailcap->{'program'}".$args);
return @rv;
}
1;
| webdev1001/webmin | mailcap/mailcap-lib.pl | Perl | bsd-3-clause | 3,915 |
# !!!!!!! DO NOT EDIT THIS FILE !!!!!!!
# This file is machine-generated by lib/unicore/mktables from the Unicode
# database, Version 8.0.0. 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';
V8
8228
8231
8943
8944
65049
65050
68342
68343
END
| operepo/ope | bin/usr/share/perl5/core_perl/unicore/lib/Lb/IN.pl | Perl | mit | 533 |
# !!!!!!! DO NOT EDIT THIS FILE !!!!!!!
# This file is machine-generated by lib/unicore/mktables from the Unicode
# database, Version 8.0.0. 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';
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183970
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195102
917760
918000
END
| operepo/ope | bin/usr/share/perl5/core_perl/unicore/lib/Perl/_PerlCh2.pl | Perl | mit | 7,896 |
#
# 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 snmp_standard::mode::listdiskspath;
use base qw(centreon::plugins::mode);
use strict;
use warnings;
my $oid_dskPath = '.1.3.6.1.4.1.2021.9.1.2';
my $oid_dskTotalLow = '.1.3.6.1.4.1.2021.9.1.11';
my $oid_dskTotalHigh = '.1.3.6.1.4.1.2021.9.1.12';
sub new {
my ($class, %options) = @_;
my $self = $class->SUPER::new(package => __PACKAGE__, %options);
bless $self, $class;
$self->{version} = '1.0';
$options{options}->add_options(arguments =>
{
"diskpath:s" => { name => 'diskpath' },
"name" => { name => 'use_name' },
"regexp" => { name => 'use_regexp' },
"regexp-isensitive" => { name => 'use_regexpi' },
"display-transform-src:s" => { name => 'display_transform_src' },
"display-transform-dst:s" => { name => 'display_transform_dst' },
"skip-total-size-zero" => { name => 'skip_total_size_zero' },
});
$self->{diskpath_id_selected} = [];
return $self;
}
sub check_options {
my ($self, %options) = @_;
$self->SUPER::init(%options);
}
sub run {
my ($self, %options) = @_;
$self->{snmp} = $options{snmp};
$self->manage_selection();
my $result = $self->get_additional_information();
foreach (sort @{$self->{diskpath_id_selected}}) {
my $display_value = $self->get_display_value(id => $_);
if (defined($result)) {
my $total_size = (($result->{$oid_dskTotalHigh . "." . $_} << 32) + $result->{$oid_dskTotalLow . "." . $_});
if ($total_size == 0) {
$self->{output}->output_add(long_msg => "Skipping disk path '" . $display_value . "': size is 0");
next;
}
}
$self->{output}->output_add(long_msg => "'" . $display_value . "' [id = " . $_ . ']');
}
$self->{output}->output_add(severity => 'OK',
short_msg => 'List disk path:');
$self->{output}->display(nolabel => 1, force_ignore_perfdata => 1, force_long_output => 1);
$self->{output}->exit();
}
sub get_additional_information {
my ($self, %options) = @_;
if (!defined($self->{option_results}->{skip_total_size_zero})) {
return undef;
}
my $oids = [$oid_dskTotalLow, $oid_dskTotalHigh];
$self->{snmp}->load(oids => $oids, instances => $self->{diskpath_id_selected});
return $self->{snmp}->get_leef();
}
sub get_display_value {
my ($self, %options) = @_;
my $value = $self->{datas}->{'dskPath_' . $options{id}};
if (defined($self->{option_results}->{display_transform_src})) {
$self->{option_results}->{display_transform_dst} = '' if (!defined($self->{option_results}->{display_transform_dst}));
eval "\$value =~ s{$self->{option_results}->{display_transform_src}}{$self->{option_results}->{display_transform_dst}}";
}
return $value;
}
sub manage_selection {
my ($self, %options) = @_;
$self->{datas} = {};
my $result = $self->{snmp}->get_table(oid => $oid_dskPath);
my $total_diskpath = 0;
foreach my $key ($self->{snmp}->oid_lex_sort(keys %$result)) {
next if ($key !~ /\.([0-9]+)$/);
$self->{datas}->{'dskPath_' . $1} = $self->{output}->to_utf8($result->{$key});
$total_diskpath = $1;
}
if (scalar(keys %{$self->{datas}}) <= 0) {
$self->{output}->add_option_msg(short_msg => "Can't get disks path...");
$self->{output}->option_exit();
}
if (!defined($self->{option_results}->{use_name}) && defined($self->{option_results}->{diskpath})) {
# get by ID
push @{$self->{diskpath_id_selected}}, $self->{option_results}->{diskpath};
my $name = $self->{datas}->{'dskPath_' . $self->{option_results}->{diskpath}};
if (!defined($name)) {
$self->{output}->add_option_msg(short_msg => "No disk path found for id '" . $self->{option_results}->{diskpath} . "'.");
$self->{output}->option_exit();
}
} else {
for (my $i = 0; $i <= $total_diskpath; $i++) {
my $filter_name = $self->{datas}->{'dskPath_' . $i};
next if (!defined($filter_name));
if (!defined($self->{option_results}->{diskpath})) {
push @{$self->{diskpath_id_selected}}, $i;
next;
}
if (defined($self->{option_results}->{use_regexp}) && defined($self->{option_results}->{use_regexpi}) && $filter_name =~ /$self->{option_results}->{diskpath}/i) {
push @{$self->{diskpath_id_selected}}, $i;
}
if (defined($self->{option_results}->{use_regexp}) && !defined($self->{option_results}->{use_regexpi}) && $filter_name =~ /$self->{option_results}->{diskpath}/) {
push @{$self->{diskpath_id_selected}}, $i;
}
if (!defined($self->{option_results}->{use_regexp}) && !defined($self->{option_results}->{use_regexpi}) && $filter_name eq $self->{option_results}->{diskpath}) {
push @{$self->{diskpath_id_selected}}, $i;
}
}
if (scalar(@{$self->{diskpath_id_selected}}) <= 0 && !defined($options{disco})) {
if (defined($self->{option_results}->{diskpath})) {
$self->{output}->add_option_msg(short_msg => "No disk path found for name '" . $self->{option_results}->{diskpath} . "'.");
} else {
$self->{output}->add_option_msg(short_msg => "No disk path found.");
}
$self->{output}->option_exit();
}
}
}
sub disco_format {
my ($self, %options) = @_;
$self->{output}->add_disco_format(elements => ['name', 'diskpathid']);
}
sub disco_show {
my ($self, %options) = @_;
$self->{snmp} = $options{snmp};
$self->manage_selection(disco => 1);
return if (scalar(@{$self->{diskpath_id_selected}}) == 0);
my $result = $self->get_additional_information();
foreach (sort @{$self->{diskpath_id_selected}}) {
if (defined($result)) {
my $total_size = (($result->{$oid_dskTotalHigh . "." . $_} << 32) + $result->{$oid_dskTotalLow . "." . $_});
next if ($total_size == 0);
}
my $display_value = $self->get_display_value(id => $_);
$self->{output}->add_disco_entry(name => $display_value,
diskpathid => $_);
}
}
1;
__END__
=head1 MODE
List disk path (UCD-SNMP-MIB).
Need to enable "includeAllDisks 10%" on snmpd.conf.
=over 8
=item B<--diskpath>
Set the disk path (number expected) ex: 1, 2,... (empty means 'check all disks path').
=item B<--name>
Allows to use disk path name with option --diskpath instead of disk path oid index.
=item B<--regexp>
Allows to use regexp to filter diskpath (with option --name).
=item B<--regexp-isensitive>
Allows to use regexp non case-sensitive (with --regexp).
=item B<--display-transform-src>
Regexp src to transform display value. (security risk!!!)
=item B<--display-transform-dst>
Regexp dst to transform display value. (security risk!!!)
=item B<--skip-total-size-zero>
Filter partitions with total size equals 0.
=back
=cut
| Shini31/centreon-plugins | snmp_standard/mode/listdiskspath.pm | Perl | apache-2.0 | 8,211 |
# !!!!!!! DO NOT EDIT THIS FILE !!!!!!!
# This file is machine-generated by lib/unicore/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';
27F0 27FF
END
| efortuna/AndroidSDKClone | ndk_experimental/prebuilt/linux-x86_64/lib/perl5/5.16.2/unicore/lib/Blk/SupArrow.pl | Perl | apache-2.0 | 433 |
#!/usr/bin/perl
# Find functions making recursive calls to themselves.
# (Multiple recursion where a() calls b() which calls a() not covered.)
#
# When the recursion depth might depend on data controlled by the attacker in
# an unbounded way, those functions should use interation instead.
#
# Typical usage: scripts/recursion.pl library/*.c
use warnings;
use strict;
use utf8;
use open qw(:std utf8);
# exclude functions that are ok:
# - mpi_write_hlp: bounded by size of mpi, a compile-time constant
# - x509_crt_verify_child: bounded by POLARSSL_X509_MAX_INTERMEDIATE_CA
my $known_ok = qr/mpi_write_hlp|x509_crt_verify_child/;
my $cur_name;
my $inside;
my @funcs;
die "Usage: $0 file.c [...]\n" unless @ARGV;
while (<>)
{
if( /^[^\/#{}\s]/ && ! /\[.*]/ ) {
chomp( $cur_name = $_ ) unless $inside;
} elsif( /^{/ && $cur_name ) {
$inside = 1;
$cur_name =~ s/.* ([^ ]*)\(.*/$1/;
} elsif( /^}/ && $inside ) {
undef $inside;
undef $cur_name;
} elsif( $inside && /\b\Q$cur_name\E\([^)]/ ) {
push @funcs, $cur_name unless /$known_ok/;
}
}
print "$_\n" for @funcs;
exit @funcs;
| GaloisInc/hacrypto | src/C/mbedtls/mbedtls-1.3.10/scripts/recursion.pl | Perl | bsd-3-clause | 1,149 |
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