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lib/App/EC2Cssh.pm view on Meta::CPAN
use AnyEvent;
use Log::Any qw/$log/;
# Config stuff.
has 'config' => ( is => 'ro', isa => 'HashRef', lazy_build => 1);
has 'config_file' => ( is => 'ro' , isa => 'Maybe[Str]');
has 'config_files' => ( is => 'ro' , isa => 'ArrayRef[Str]' , lazy_build => 1);
# Run options stuff
has 'set' => ( is => 'ro' , isa => 'Str', required => 1 );
has 'demux_command' => ( is => 'ro', isa => 'Maybe[Str]', required => 0, predicate => 'has_demux_command' );
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lib/App/JESP.pm view on Meta::CPAN
};
});
has 'dbix_simple' => ( is => 'ro', isa => 'DBIx::Simple', lazy_build => 1);
has 'patches_table_name' => ( is => 'ro', isa => 'Str' , lazy_build => 1);
has 'meta_patches' => ( is => 'ro', isa => 'ArrayRef[HashRef]',
lazy_build => 1 );
has 'plan' => ( is => 'ro', isa => 'App::JESP::Plan', lazy_build => 1);
has 'driver' => ( is => 'ro', isa => 'App::JESP::Driver', lazy_build => 1 );
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lib/App/JIRAPrint.pm view on Meta::CPAN
}
};
# Config stuff.
has 'config' => ( is => 'ro', isa => 'HashRef', lazy_build => 1);
has 'config_files' => ( is => 'ro' , isa => 'ArrayRef[Str]' , lazy_build => 1);
has 'shared_directory' => ( is => 'ro', isa => 'Str', lazy_build => 1);
has 'template_file' => ( is => 'ro', isa => 'Str', lazy_build => 1);
lib/App/JIRAPrint.pm view on Meta::CPAN
has 'project' => ( is => 'ro', isa => 'Str' , lazy_build => 1 );
has 'sprint' => ( is => 'ro', isa => 'Str' , lazy_build => 1 );
has 'maxissues' => ( is => 'ro', isa => 'Int' , lazy_build => 1);
has 'jql' => ( is => 'ro', isa => 'Str', lazy_build => 1);
has 'fields' => ( is => 'ro', isa => 'ArrayRef[Str]', lazy_build => 1 );
# Objects
has 'jira' => ( is => 'ro', isa => 'JIRA::REST', lazy_build => 1);
has 'tt' => ( is => 'ro', isa => 'Template', lazy_build => 1);
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.claude/skills/perl-moose/SKILL.md view on Meta::CPAN
## Pattern 7 – Attribute Options Cheatsheet
```perl
has name => (is => 'ro', required => 1);
has tags => (is => 'ro', isa => 'ArrayRef[Str]', default => sub { [] }); # ALWAYS coderef for refs
has content => (is => 'lazy'); # built on first access
sub _build_content { "generated: " . $_[0]->name }
has status => (
is => 'rw',
.claude/skills/perl-moose/SKILL.md view on Meta::CPAN
via { int($_) };
# Or use Type::Tiny (recommended — works with both Moo and Moose):
use Types::Standard qw(Str Int ArrayRef InstanceOf);
has name => (is => 'ro', isa => Str);
has items => (is => 'ro', isa => ArrayRef[Str], default => sub { [] });
```
Prefer `Type::Tiny` / `Types::Standard` — portable between Moo and Moose, better error messages.
---
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t/new_target.t view on Meta::CPAN
package App::SpreadRevolutionaryDate::Target::Ezln;
use Moose;
with 'App::SpreadRevolutionaryDate::Target' => {worker => 'Bool'};
use namespace::autoclean;
has 'subcomandantes' => (is => 'ro', isa => 'ArrayRef[Str]', required => 1);
has 'land' => (is => 'ro', isa => 'Str', required => 1);
around BUILDARGS => sub {
my ($orig, $class) = @_;
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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 $_parser = DateTime::Format::Strptime->new(
pattern => '%a %b %d %T %z %Y',
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.claude/skills/perl-moo/SKILL.md view on Meta::CPAN
Moo has no built-in type system. `isa` takes a coderef:
```perl
use Types::Standard qw(Str Int ArrayRef);
has name => (is => 'ro', isa => Str);
has tags => (is => 'ro', isa => ArrayRef[Str], default => sub { [] });
```
`Type::Tiny` / `Types::Standard` is the official recommendation in Moo docs (replaces `MooseX::Types`).
---
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lib/Array/GroupBy.pm view on Meta::CPAN
package Patient;
use Moose;
has last => (is => 'ro', isa => 'Str');
has first => (is => 'ro', isa => 'Str');
has Visits => (is => 'ro', isa => 'ArrayRef[Visit]');
no Moose;
use DBI;
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lib/Array/To/Moose.pm view on Meta::CPAN
package CarOwner;
use Moose;
has 'last' => (is => 'ro', isa => 'Str');
has 'first' => (is => 'ro', isa => 'Str');
has 'Cars' => (is => 'ro', isa => ArrayRef[Car]');
...
# in package main:
lib/Array/To/Moose.pm view on Meta::CPAN
package CarOwner;
use Moose;
has 'last' => (is => 'ro', isa => 'Str' );
has 'first' => (is => 'ro', isa => 'Str' );
has 'Cars' => (is => 'ro', isa => 'HashRef[Car]'); # Was 'ArrayRef[Car]'
and noting that the car C<make> is unique for each person in the C<$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(
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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 {
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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 = @_;
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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;
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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;
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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 { {} } );
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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' );
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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' );
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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 $CallContext;
our %return_counts = (
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lib/Bio/MLST/Blast/BlastN.pm view on Meta::CPAN
use List::Util qw(reduce max min);
# input variables
has 'blast_database' => ( is => 'ro', isa => 'Str', required => 1 );
has 'query_file' => ( is => 'ro', isa => 'Str', required => 1 );
has 'word_sizes' => ( is => 'ro', isa => 'HashRef', required => 1 );
has 'exec' => ( is => 'ro', isa => 'Bio::MLST::Executable', default => 'blastn' );
has 'perc_identity' => ( is => 'ro', isa => 'Int', default => 0 );
# Generated
has 'top_hit' => ( is => 'ro', isa => 'Maybe[HashRef]', lazy => 1, builder => '_build_top_hit' );
sub _build_hit
{
my($self, $line) = @_;
chomp($line);
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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 {
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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,$cmd_version );
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lib/Bio/Roary/AccessoryBinaryFasta.pm view on Meta::CPAN
use Bio::Roary::AnalyseGroups;
use Bio::Roary::Exceptions;
use Bio::SeqIO;
use File::Basename;
has 'input_files' => ( is => 'ro', isa => 'ArrayRef', required => 1 );
has 'annotate_groups_obj' => ( is => 'ro', isa => 'Bio::Roary::AnnotateGroups', required => 1 );
has 'analyse_groups_obj' => ( is => 'ro', isa => 'Bio::Roary::AnalyseGroups', required => 1 );
has 'output_filename' => ( is => 'ro', isa => 'Str', default => 'accessory_binary_genes.fa' );
has 'lower_bound_percentage' => ( is => 'ro', isa => 'Int', default => 5 );
has 'upper_bound_percentage' => ( is => 'ro', isa => 'Int', default => 5 );
has 'max_accessory_to_include' => ( is => 'ro', isa => 'Int', default => 4000 );
has 'groups_to_files' => ( is => 'ro', isa => 'HashRef', lazy => 1, builder => '_build__groups_to_files' );
has '_lower_bound_value' => ( is => 'ro', isa => 'Int', lazy => 1, builder => '_build__lower_bound_value' );
has '_upper_bound_value' => ( is => 'ro', isa => 'Int', lazy => 1, builder => '_build__upper_bound_value' );
sub _build__groups_to_files {
my ($self) = @_;
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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 );
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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' );
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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
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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,
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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' );
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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',
);
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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',
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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);
}
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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;