view release on metacpan or  search on metacpan

lib/App/Twimap/Tweet.pm  view on Meta::CPAN

use DateTime::Format::Strptime;
use Email::Date::Format qw(email_date);
use HTML::Entities;
use Text::Wrap qw(wrap);

has 'data'        => ( is => 'ro', isa => 'HashRef', required => 1 );
has 'expand_urls' => ( is => 'ro', isa => 'Bool',    default  => 1 );
has 'oembed_urls' => ( is => 'ro', isa => 'Bool',    default  => 1 );

my $_parser = DateTime::Format::Strptime->new(
    pattern  => '%a %b %d %T %z %Y',

 view release on metacpan or  search on metacpan

lib/Array/GroupBy.pm  view on Meta::CPAN

  package Patient;
  use Moose;
  has last      => (is => 'ro', isa => 'Str'); 
  has first     => (is => 'ro', isa => 'Str'); 
  has Visits    => (is => 'ro', isa => 'ArrayRef[Visit]');

  no Moose;

  use DBI;

 view release on metacpan or  search on metacpan

lib/Array/To/Moose.pm  view on Meta::CPAN

  package CarOwner;
  use Moose;

  has 'last'  => (is => 'ro', isa => 'Str');
  has 'first' => (is => 'ro', isa => 'Str');
  has 'Cars'  => (is => 'ro', isa => ArrayRef[Car]');

  ...

  # in package main:

lib/Array/To/Moose.pm  view on Meta::CPAN

  package CarOwner;
  use Moose;

  has 'last'  => (is => 'ro', isa => 'Str'         );
  has 'first' => (is => 'ro', isa => 'Str'         );
  has 'Cars'  => (is => 'ro', isa => 'HashRef[Car]'); # Was 'ArrayRef[Car]'

and noting that the car C<make> is unique for each person in the C<$data> dataset, we
construct the reference to an array of objects with the call:

  $CarOwners = array_to_moose(

lib/Array/To/Moose.pm  view on Meta::CPAN

  package SimpleCarOwner;
  use Moose;

  has 'last'      => (is => 'ro', isa => 'Str'          );
  has 'first'     => (is => 'ro', isa => 'Str'          );
  has 'CarMakers' => (is => 'ro', isa => 'ArrayRef[Str]');

Using the same dataset from Example 1a, we construct an arrayref
C<SimpleCarOwner> objects as:

  $SimpleCarOwners = array_to_moose(

 view release on metacpan or  search on metacpan

lib/Attean/API/Parser.pm  view on Meta::CPAN

	
	has 'handler' => (is => 'rw', isa => CodeRef, default => sub { sub {} });
	has 'lazy_iris' => (is => 'rw', isa => Bool, default => 0);
	
	requires 'canonical_media_type'; # => (is => 'ro', isa => 'Str', init_arg => undef);
	requires 'media_types'; # => (is => 'ro', isa => 'ArrayRef[Str]', init_arg => undef);
	requires 'handled_type'; # => (is => 'ro', isa => 'Type::Tiny', init_arg => undef);
	requires 'file_extensions'; # => (is => 'ro', isa => 'ArrayRef[Str]', init_arg => undef);
	
=item C<< new_iri( value => $value ) >>

Constructs and returns a new L<Attean::IRI> object, respecting the parser's
C<lazy_iris> attribute.

lib/Attean/API/Parser.pm  view on Meta::CPAN

	use UUID::Tiny ':std';
	use Data::Dumper;
	use Moo::Role;
	
	with 'Attean::API::Parser';
	has 'blank_nodes'	=> (is => 'ro', isa => Maybe[HashRef[ConsumerOf['Attean::API::Blank']]]);
	has 'parse_id'		=> (is => 'rw', default => sub { unpack('H*', create_uuid()) });
	has 'enable_cdt_rewriting' => (is => 'rw', isa => Bool, default => 1);

	foreach my $method (qw(parse_iter_from_io parse_iter_from_bytes parse_cb_from_io parse_cb_from_bytes)) {
		around $method => sub {

 view release on metacpan or  search on metacpan

lib/AtteanX/Endpoint.pm  view on Meta::CPAN

	use Moo;
	use Types::Standard qw(Str HashRef);
	use namespace::clean;

	has 'message'	=> (is => 'ro', isa => Str, required => 1);
	has 'details'	=> (is => 'ro', isa => HashRef, default => sub { +{} });
	has 'uri'		=> (is => 'ro', isa => Str);
}

package AtteanX::Endpoint::Error {
	use Moo;

lib/AtteanX/Endpoint.pm  view on Meta::CPAN

		default => sub {
			Attean::IDPQueryPlanner->new();
		}
	);
	has 'model' => (is => 'ro', isa => ConsumerOf['Attean::API::Model'], required => 1);
	has 'conf'	=> (is => 'ro', isa => HashRef, required => 1);
	has 'graph'	=> (is => 'ro', isa => ConsumerOf['Attean::API::IRI'], required => 1);
	
	sub BUILDARGS {
		my $class		= shift;
		my @params = @_;

 view release on metacpan or  search on metacpan

lib/AtteanX/Serializer/RDFa.pm  view on Meta::CPAN

with 'Attean::API::TripleSerializer';
with 'Attean::API::AbbreviatingSerializer';

has 'style' => (is => 'ro', isa => Maybe[Str]); # TODO: might be improved with OptList?

has 'generator_options' => (is => 'ro', isa => HashRef, default => sub { return {} });

has _opts => (is => 'rw', isa => HashRef, lazy => 1, builder => '_build_opts');

sub _build_opts {
  my $self = shift;

 view release on metacpan or  search on metacpan

lib/AtteanX/Store/DBI.pm  view on Meta::CPAN

	use Type::Tiny::Role;
	use Types::Standard qw(HashRef ArrayRef InstanceOf Str);
	use namespace::clean;
	
	has store			=> (is => 'ro', isa => InstanceOf['AtteanX::Store::DBI'], required => 1);
	has rename_mapping	=> (is => 'ro', isa => HashRef[Str], default => sub { +{} });
	has variables		=> (is => 'ro', isa => HashRef, required => 1);
	has bindings		=> (is => 'ro', isa => ArrayRef, required => 1);
	has select			=> (is => 'ro', isa => ArrayRef, required => 1);
	has where			=> (is => 'ro', isa => ArrayRef, required => 1);
	has tables			=> (is => 'ro', isa => ArrayRef[ArrayRef[Str]], required => 1);
	
	with 'Attean::API::BindingSubstitutionPlan', 'Attean::API::NullaryQueryTree';
	
	sub plan_as_string {
		my $self	= shift;

 view release on metacpan or  search on metacpan

lib/Auth/Kokolores/Config.pm  view on Meta::CPAN

has 'max_requests' => ( is => 'rw', isa => 'Int', default => '1000' );

has 'satisfy' => ( is => 'rw', isa => 'Str', default => 'all' );

has 'overwrittable_attributes' => (
  is => 'ro', isa => 'ArrayRef[Str]', default => sub { [
    'log_level', 'log_file'
  ] },
);
has 'net_server_attributes' => (
  is => 'ro', isa => 'ArrayRef[Str]', default => sub { [
    'syslog_ident', 'syslog_facility', 'user', 'group',
    'min_servers', 'min_spare_servers', 'max_spare_servers', 'max_servers',
    'max_requests', 'pid_file',
  ] },
);
has 'kokolores_attributes' => (
  is => 'ro', isa => 'ArrayRef[Str]', default => sub { [
    'socket_path', 'socket_mode', 'satisfy', 'protocol',
  ] },
);

has 'Plugin' => ( is => 'rw', isa => 'HashRef', default => sub { {} } );

 view release on metacpan or  search on metacpan

lib/Bio/AutomatedAnnotation/CommandLine/AnnotateBacteria.pm  view on Meta::CPAN

use Moose;
use Getopt::Long qw(GetOptionsFromArray);
use Bio::AutomatedAnnotation;

has 'args'        => ( is => 'ro', isa => 'ArrayRef', required => 1 );
has 'script_name' => ( is => 'ro', isa => 'Str',      required => 1 );
has 'help'        => ( is => 'rw', isa => 'Bool',     default  => 0 );

has 'sample_name'       => ( is => 'rw', isa => 'Str'  );
has 'dbdir'             => ( is => 'rw', isa => 'Str', default => '/lustre/scratch118/infgen/pathogen/pathpipe/prokka'  );

 view release on metacpan or  search on metacpan

lib/Bio/InterProScanWrapper/CommandLine/AnnotateEukaryotes.pm  view on Meta::CPAN

use Getopt::Long qw(GetOptionsFromArray);
use Cwd;
use File::Basename;
use Bio::InterProScanWrapper;

has 'args'                    => ( is => 'ro', isa => 'ArrayRef', required => 1 );
has 'script_name'             => ( is => 'ro', isa => 'Str',      required => 1 );
has 'help'                    => ( is => 'rw', isa => 'Bool',     default  => 0 );
has 'cpus'                    => ( is => 'rw', isa => 'Int',      default  => 100 );
has 'exec_script'             => ( is => 'rw', isa => 'Str',      default  => '/software/pathogen/external/apps/usr/local/iprscan-5.0.7/interproscan.sh' );
has 'proteins_file'           => ( is => 'rw', isa => 'Str' );

 view release on metacpan or  search on metacpan

lib/Bio/KBase/CDMI/Service.pm  view on Meta::CPAN

use Data::Dumper;
use Moose;

extends 'RPC::Any::Server::JSONRPC::PSGI';

has 'instance_dispatch' => (is => 'ro', isa => 'HashRef');
has 'user_auth' => (is => 'ro', isa => 'UserAuth');
has 'valid_methods' => (is => 'ro', isa => 'HashRef', lazy => 1,
			builder => '_build_valid_methods');

our $CallContext;

our %return_counts = (

 view release on metacpan or  search on metacpan

lib/Bio/MLST/Blast/BlastN.pm  view on Meta::CPAN

use List::Util qw(reduce max min);

# input variables
has 'blast_database'     => ( is => 'ro', isa => 'Str', required => 1 ); 
has 'query_file'         => ( is => 'ro', isa => 'Str', required => 1 ); 
has 'word_sizes'         => ( is => 'ro', isa => 'HashRef', required => 1 ); 
has 'exec'               => ( is => 'ro', isa => 'Bio::MLST::Executable', default  => 'blastn' ); 
has 'perc_identity'      => ( is => 'ro', isa => 'Int', default  => 0 );

# Generated
has 'top_hit'           => ( is => 'ro', isa => 'Maybe[HashRef]', lazy => 1,  builder => '_build_top_hit' ); 

sub _build_hit
{
  my($self, $line) = @_;
  chomp($line);

 view release on metacpan or  search on metacpan

lib/Bio/Pipeline/Comparison/Generate/Evolve.pm  view on Meta::CPAN

has 'input_filename'  => ( is => 'ro', isa => 'Str', required => 1 );
has 'output_filename' => ( is => 'ro', isa => 'Str', lazy => 1, builder => '_build_output_filename' );
has 'vcf_output_filename' => ( is => 'ro', isa => 'Str', lazy => 1, builder => '_build_vcf_output_filename' );

has '_base_change_probability' => ( is => 'ro', isa => 'HashRef', lazy => 1, builder => '_build__base_change_probability' );
has '_snp_rate'                => ( is => 'ro', isa => 'Num', default => '0.005' );
has '_vcf_writer'              => ( is => 'ro', isa => 'Bio::Pipeline::Comparison::Generate::VCFWriter', lazy => 1, builder => '_build__vcf_writer' );

# placeholder for proper evolutionary model
sub evolve {

 view release on metacpan or  search on metacpan

lib/Bio/RetrieveAssemblies.pm  view on Meta::CPAN

has 'output_directory' => ( is => 'rw', isa => 'Str', default => 'downloaded_files' );
has 'file_type'        => ( is => 'rw', isa => 'Str', default => 'genbank' );
has 'organism_type'    => ( is => 'rw', isa => 'Str', default => 'BCT' );
has 'query'            => ( is => 'rw', isa => 'Str',      default  => '*' );
has 'annotation'       => ( is => 'rw', isa => 'Bool',     default  => 0 );
has 'args'             => ( is => 'ro', isa => 'ArrayRef', required => 1 );
has 'script_name'      => ( is => 'ro', isa => 'Str', required => 1 );

sub BUILD {
    my ($self) = @_;
    my ( $help, $file_type, $output_directory, $organism_type,$query,$annotation,$verbose,$cmd_version );

 view release on metacpan or  search on metacpan

lib/Bio/Roary/AccessoryBinaryFasta.pm  view on Meta::CPAN

use Bio::Roary::AnalyseGroups;
use Bio::Roary::Exceptions;
use Bio::SeqIO;
use File::Basename;

has 'input_files'            => ( is => 'ro', isa => 'ArrayRef',                   required => 1 );
has 'annotate_groups_obj'    => ( is => 'ro', isa => 'Bio::Roary::AnnotateGroups', required => 1 );
has 'analyse_groups_obj'     => ( is => 'ro', isa => 'Bio::Roary::AnalyseGroups',  required => 1 );
has 'output_filename'        => ( is => 'ro', isa => 'Str',                        default  => 'accessory_binary_genes.fa' );
has 'lower_bound_percentage' => ( is => 'ro', isa => 'Int',                        default  => 5 );
has 'upper_bound_percentage' => ( is => 'ro', isa => 'Int',                        default  => 5 );
has 'max_accessory_to_include' => ( is => 'ro', isa => 'Int',                      default  => 4000 );
has 'groups_to_files'        => ( is => 'ro', isa => 'HashRef',                    lazy     => 1, builder => '_build__groups_to_files' );
has '_lower_bound_value'     => ( is => 'ro', isa => 'Int',                        lazy     => 1, builder => '_build__lower_bound_value' );
has '_upper_bound_value'     => ( is => 'ro', isa => 'Int',                        lazy     => 1, builder => '_build__upper_bound_value' );

sub _build__groups_to_files {
    my ($self) = @_;

 view release on metacpan or  search on metacpan

lib/Bio/Tradis/CommandLine/AddTags.pm  view on Meta::CPAN

use Moose;
use Getopt::Long qw(GetOptionsFromArray);
use Cwd 'abs_path';
use Bio::Tradis::AddTagsToSeq;

has 'args'        => ( is => 'ro', isa => 'ArrayRef', required => 1 );
has 'script_name' => ( is => 'ro', isa => 'Str',      required => 1 );
has 'bamfile'     => ( is => 'rw', isa => 'Str',      required => 0 );
has 'help'        => ( is => 'rw', isa => 'Bool',     required => 0 );
has 'outfile'     => ( is => 'rw', isa => 'Str',      required => 0 );

 view release on metacpan or  search on metacpan

lib/Bio/VertRes/Config/CommandLine/Common.pm  view on Meta::CPAN

use Getopt::Long qw(GetOptionsFromArray);
use Bio::VertRes::Config::CommandLine::LogParameters;
use Bio::VertRes::Config::CommandLine::ConstructLimits;
use Bio::VertRes::Config::Exceptions;

has 'args'        => ( is => 'ro', isa => 'ArrayRef', required => 1 );
has 'script_name' => ( is => 'ro', isa => 'Str',      required => 1 );

has 'database'    => ( is => 'rw', isa => 'Str', default => 'pathogen_prok_track' );
has 'config_base' => ( is => 'rw', isa => 'Str', default => '/nfs/pathnfs05/conf' );
has 'root_base'   => ( is => 'rw', isa => 'Str', default => '/lustre/scratch108/pathogen/pathpipe' );

 view release on metacpan or  search on metacpan

lib/Bio/AssemblyImprovement/Assemble/SGA/Main.pm  view on Meta::CPAN

use Bio::AssemblyImprovement::Assemble::SGA::IndexAndCorrectReads;

with 'Bio::AssemblyImprovement::Scaffold::SSpace::TempDirectoryRole';
with 'Bio::AssemblyImprovement::Util::ZipFileRole';

has 'input_files'       => ( is => 'ro', isa => 'ArrayRef' , required => 1);

# Parameters for preprocessing
has 'min_length'	   => ( is => 'ro', isa => 'Num', default => 51);
has 'quality_trim'	   => ( is => 'ro', isa => 'Num', default => 3);
has 'pe_mode'		   => ( is => 'ro', isa => 'Num', default => 2); #We set default to 2 as the pipeline will almost always send in an interleaved fastq file

 view release on metacpan or  search on metacpan

lib/Blio.pm  view on Meta::CPAN

has 'force' => (is=>'ro',isa=>'Bool',default=>0);
has 'quiet' => (is=>'ro',isa=>'Bool',default=>0);
has 'recent' => (is=>'ro',isa=>'Bool',default=>0);

has 'nodes_by_url' => ( is => 'ro', isa => 'HashRef', default => sub { {} } ,traits  => [ 'NoGetopt' ]);
has 'tree' => (
    is      => 'ro',
    isa     => 'ArrayRef[Blio::Node]',
    default => sub { [] },
    traits  => ['Array', 'NoGetopt'],

lib/Blio.pm  view on Meta::CPAN

        WRAPPER=>'wrapper.tt',
        ENCODING     => 'UTF8',
    });
}

has 'nodes_by_date' => (is=>'ro', isa=>'ArrayRef',lazy_build=>1,traits  => [ 'NoGetopt' ]);
sub _build_nodes_by_date {
    my $self = shift;

    my @sorted =
        map { $_->[0] }
        sort { $b->[1] <=> $a->[1] }
        map { [$_ => $_->date->epoch] }
        values %{$self->nodes_by_url};
    return \@sorted;
}
has 'stash' => (is=>'ro',isa=>'HashRef',default=>sub {{}},traits  => [ 'NoGetopt' ]);

has 'tagindex' => (
    is=>'rw',
    isa=>'Blio::Node',
    lazy_build=>1,

 view release on metacpan or  search on metacpan

t/00-tsvstream.t  view on Meta::CPAN

use Moose;
use namespace::autoclean;
use MooseX::ClassAttribute;

class_has '_fields' => (is => 'ro', isa => 'ArrayRef', default => sub { [ qw(foo bar) ] } );

with 'BoutrosLab::TSVStream::IO::Role::Fixed';

has 'foo'    => ( is => 'rw', isa => 'Str' );
has 'bar'    => ( is => 'rw', isa => 'Str' );

 view release on metacpan or  search on metacpan

lib/Bread/Board/LazyLoader/Obj.pm  view on Meta::CPAN

# remember the subs returned from builder files
has cache_codes => ( is => 'ro', default => 1 );

# builders (files and codes) for current container
has builders => ( is => 'ro', isa => 'ArrayRef', default => sub { [] }, );

has container_class => (
    is      => 'ro',
    default => 'Bread::Board::Container',
);

 view release on metacpan or  search on metacpan

t/048_array_deps.t  view on Meta::CPAN

    package ListOfItems;
    use Moose;

    sub as_string { join ',',map {$_->my_name} @{shift->items} }

    has 'items' => (is => 'ro', isa => 'ArrayRef');
}

{
    my $s = Bread::Board::ConstructorInjection->new(
        name => 'list_of_items',

 view release on metacpan or  search on metacpan

lib/Business/CompanyDesignator.pm  view on Meta::CPAN

# data is the raw dataset as loaded from datafile, keyed by long designator
has data => ( is => 'ro', lazy_build => 1 );

# regex_cache is a cache of regexes by language and type, since they're expensive to build
has 'regex_cache' => ( is => 'ro', isa => 'HashRef', default => sub { {} } );

# abbr_long_map is a hash mapping abbreviations (strings) back to an arrayref of
# long designators (since abbreviations are not necessarily unique)
has 'abbr_long_map' => ( is => 'ro', isa => 'HashRef', lazy_build => 1 );

# pattern_string_map is a hash mapping patterns back to their source string,
# since we do things like add additional patterns without diacritics
has 'pattern_string_map' => ( is => 'ro', isa => 'HashRef', default => sub { {} } );
# pattern_string_map_lang is a hash of hashes, mapping language codes to hashes
# of patterns back to their source string
has 'pattern_string_map_lang' => ( is => 'ro', isa => 'HashRef', default => sub { {} } );

sub _build_data {
  my $self = shift;
  YAML::LoadFile($self->datafile);
}

 view release on metacpan or  search on metacpan

lib/CHI/Driver/CacheCache.pm  view on Meta::CPAN

use warnings;

extends 'CHI::Driver::Base::CacheContainer';

has 'cc_class'   => ( is => 'ro', isa => Str, required => 1 );
has 'cc_options' => ( is => 'ro', isa => HashRef, required => 1 );

sub BUILD {
    my ( $self, $params ) = @_;

    $self->{_contained_cache} = $self->_build_contained_cache;

 view release on metacpan or  search on metacpan

lib/CLI/Gwrap.pm  view on Meta::CPAN

has 'gwrapper'      => (is => 'rw');
has 'columns'       => (is => 'rw', isa => Int, default => 3);
has 'verbatim'      => (is => 'ro', isa => Bool);
has 'help'          => (is => 'ro', isa => Str);
has 'persist'       => (is => 'ro', isa => Bool);
has 'opts'          => (is => 'ro', isa => ArrayRef[InstanceOf['CLI::Gwrap::Opt']]);
has 'advanced'      => (is => 'ro', isa => ArrayRef[InstanceOf['CLI::Gwrap::Opt']]);
has 'exec_callback' => (is => 'ro', isa => CodeRef);
has 'timeout'       => (is => 'ro', isa => Int);

sub BUILD {
    my ($self, $params) = @_;

 view release on metacpan or  search on metacpan

lib/CMS/Drupal/Modules/MembershipEntity/Membership.pm  view on Meta::CPAN

has changed   => ( is => 'ro', isa => Int, required => 1 );
has uid       => ( is => 'ro', isa => Int, required => 1 );
has status    => ( is => 'ro', isa => Enum[ qw/0 1 2 3/ ], required => 1 );
has member_id => ( is => 'ro', isa => Str, required => 1 );
has type      => ( is => 'ro', isa => Str, required => 1 );
has terms     => ( is => 'ro', isa => HashRef, required => 1 );


sub is_expired {
  my $self = shift;
  $self->{'_is_expired'} = $self->{'status'} eq '0' ? 1 : 0;

 view release on metacpan or  search on metacpan

lib/CPAN/Visitor.pm  view on Meta::CPAN

use MooseX::Params::Validate 0.13;
use namespace::autoclean 0.09 ;

has 'cpan'  => ( is => 'ro', required => 1 );
has 'quiet' => ( is => 'ro', default => 0 );
has 'stash' => ( is => 'ro', isa => 'HashRef',  default => sub { {} } );
has 'files' => ( is => 'ro', isa => 'ArrayRef', default => sub { [] } );

sub BUILD {
  my $self = shift;
  unless (
    -d $self->cpan &&

 view release on metacpan or  search on metacpan

lib/CSS/Scopifier/Group.pm  view on Meta::CPAN

use Path::Class qw(file);
use Text::Balanced qw(extract_bracketed);

has 'group_name', is => 'ro', isa => Maybe[Str], default => sub {undef};
has 'local',      is => 'ro', isa => InstanceOf['CSS::Scopifier'], default => sub { CSS::Scopifier->new };
has '_members',   is => 'ro', isa => ArrayRef, default => sub {[]};

sub scopify {
  my $self = shift;
  $_->scopify(@_) for ($self->local,@{$self->_members});
  return 1;

 view release on metacpan or  search on metacpan

lib/Caller/Easy.pm  view on Meta::CPAN

has 'wantarray'  => ( is => 'ro', writer => '_set_wantarray', isa => 'Bool' );
has 'evaltext'   => ( is => 'ro', writer => '_set_evaltext', isa => 'Str' );
has 'is_require' => ( is => 'ro', writer => '_set_is_require', isa => 'Bool' );
has 'hints'      => ( is => 'ro', writer => '_set_hints', isa => 'Num' );
has 'bitmask'    => ( is => 'ro', writer => '_set_bitmask', isa => 'Str' );
has 'hinthash'   => ( is => 'ro', writer => '_set_hinthash', isa => 'Maybe[HashRef]' );
has 'args'       => ( is => 'ro', writer => '_set_args', isa => 'Maybe[ArrayRef]' );

around BUILDARGS => sub {
    my $orig  = shift;
    my $class = shift;

 view release on metacpan or  search on metacpan

lib/Catalyst/Authentication/Credential/AuthTkt.pm  view on Meta::CPAN

package Catalyst::Authentication::Credential::AuthTkt;
use Moose;
use namespace::autoclean;

has 'config' => ( is => 'ro', isa => 'HashRef' );

our $VERSION = '0.17';

=head1 NAME