Bio-MLST-Check

 view release on metacpan or  search on metacpan

META.json  view on Meta::CPAN

            "Bio::SimpleAlign" : "0",
            "Cwd" : "0",
            "Data::Dumper" : "0",
            "Exporter" : "0",
            "File::Basename" : "0",
            "File::Copy" : "0",
            "File::Path" : "2.06",
            "File::Temp" : "0",
            "File::Which" : "0",
            "Getopt::Long" : "0",
            "HTTP::Request" : "0",
            "LWP::Simple" : "0",
            "LWP::UserAgent" : "0",
            "List::Util" : "0",
            "Moose" : "0",
            "Moose::Role" : "0",
            "Moose::Util::TypeConstraints" : "0",
            "POSIX" : "0",
            "Parallel::ForkManager" : "0",
            "Regexp::Common" : "0",
            "Text::CSV" : "0",

META.yml  view on Meta::CPAN

  Bio::SimpleAlign: 0
  Cwd: 0
  Data::Dumper: 0
  Exporter: 0
  File::Basename: 0
  File::Copy: 0
  File::Path: 2.06
  File::Temp: 0
  File::Which: 0
  Getopt::Long: 0
  HTTP::Request: 0
  LWP::Simple: 0
  LWP::UserAgent: 0
  List::Util: 0
  Moose: 0
  Moose::Role: 0
  Moose::Util::TypeConstraints: 0
  POSIX: 0
  Parallel::ForkManager: 0
  Regexp::Common: 0
  Text::CSV: 0

Makefile.PL  view on Meta::CPAN

    "Bio::SimpleAlign" => 0,
    "Cwd" => 0,
    "Data::Dumper" => 0,
    "Exporter" => 0,
    "File::Basename" => 0,
    "File::Copy" => 0,
    "File::Path" => "2.06",
    "File::Temp" => 0,
    "File::Which" => 0,
    "Getopt::Long" => 0,
    "HTTP::Request" => 0,
    "LWP::Simple" => 0,
    "LWP::UserAgent" => 0,
    "List::Util" => 0,
    "Moose" => 0,
    "Moose::Role" => 0,
    "Moose::Util::TypeConstraints" => 0,
    "POSIX" => 0,
    "Parallel::ForkManager" => 0,
    "Regexp::Common" => 0,
    "Text::CSV" => 0,

Makefile.PL  view on Meta::CPAN

  "ExtUtils::MakeMaker" => 0,
  "File::Basename" => 0,
  "File::Copy" => 0,
  "File::Path" => "2.06",
  "File::Slurp" => 0,
  "File::Spec" => 0,
  "File::Temp" => 0,
  "File::Touch" => 0,
  "File::Which" => 0,
  "Getopt::Long" => 0,
  "HTTP::Request" => 0,
  "HTTP::Status" => 0,
  "IO::Scalar" => 0,
  "LWP::Simple" => 0,
  "LWP::UserAgent" => 0,
  "List::Util" => 0,
  "Moose" => 0,
  "Moose::Role" => 0,
  "Moose::Util::TypeConstraints" => 0,
  "POSIX" => 0,
  "Parallel::ForkManager" => 0,

lib/Bio/MLST/DatabaseSettings.pm  view on Meta::CPAN

package Bio::MLST::DatabaseSettings;
# ABSTRACT: Read in an XML file of settings and return a hash with the values.
$Bio::MLST::DatabaseSettings::VERSION = '2.1.1706216';

use Moose;
use XML::LibXML;
use LWP::UserAgent;
use HTTP::Request;

has 'filename'          => ( is => 'ro', isa => 'Str', required => 1 );

sub generate_dom
{
	my($self, $location ) = @_;
	
	# local file and remote files need to be treated differently
	if ( !( $location =~ /(http|ftp)/ ) ) {
		return XML::LibXML->load_xml( location => $location );	
	}
	else
	{
		# its a remote file so download content
	        my $ua = LWP::UserAgent->new;
		if(defined($ENV{HTTPS_PROXY}))
		{
	        	$ua->proxy( [ 'http', 'https' ], $ENV{HTTPS_PROXY} );
		}
	        my $req = HTTP::Request->new( GET => $location );
	        my $res = $ua->request($req);
	        $res->is_success or die "Could not connect to $location\n";
		XML::LibXML->load_xml( string => $res->content );
	}
}

sub settings
{
  my($self) = @_;
  my %databases_attributes;

t/00-report-prereqs.dd  view on Meta::CPAN

                                      'Bio::SimpleAlign' => '0',
                                      'Cwd' => '0',
                                      'Data::Dumper' => '0',
                                      'Exporter' => '0',
                                      'File::Basename' => '0',
                                      'File::Copy' => '0',
                                      'File::Path' => '2.06',
                                      'File::Temp' => '0',
                                      'File::Which' => '0',
                                      'Getopt::Long' => '0',
                                      'HTTP::Request' => '0',
                                      'LWP::Simple' => '0',
                                      'LWP::UserAgent' => '0',
                                      'List::Util' => '0',
                                      'Moose' => '0',
                                      'Moose::Role' => '0',
                                      'Moose::Util::TypeConstraints' => '0',
                                      'POSIX' => '0',
                                      'Parallel::ForkManager' => '0',
                                      'Regexp::Common' => '0',
                                      'Text::CSV' => '0',