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lib/Bio/MLST/Download/Database.pm  view on Meta::CPAN

with 'Bio::MLST::Download::Downloadable';

has 'database_attributes'  => ( is => 'ro', isa => 'HashRef', required => 1 );
has 'base_directory'       => ( is => 'ro', isa => 'Str',     required => 1 );
has 'species'              => ( is => 'ro', isa => 'Str',     required => 1 );

has 'destination_directory' => ( is => 'ro', isa => 'Str',     lazy => 1, builder => '_build_destination_directory' );


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

  for my $allele_file (@{$self->database_attributes->{alleles}})
  {
    $self->_download_file($allele_file,join('/',($self->destination_directory,'alleles')));
  }
  $self->_download_file($self->database_attributes->{profiles},join('/',($self->destination_directory,'profiles')));

  1;

lib/Bio/MLST/Download/Databases.pm  view on Meta::CPAN

use File::Path qw(make_path rmtree);
use POSIX qw(strftime);

has 'databases_attributes' => ( is => 'ro', isa => 'HashRef', required => 1 );
has 'base_directory'       => ( is => 'ro', isa => 'Str',     required => 1 );

has 'parallel_processes'   => ( is => 'ro', isa => 'Int',     default => 0 );

has '_species_to_exclude'  => ( is => 'ro', isa => 'Str',     default => 'Pediococcus' );

sub update {
   my($self) = @_;
   my $paths_to_database_updates = $self->databases_attributes;
   my $species_to_exclude = $self->_species_to_exclude;
   my $temp_folder = strftime "temp_%Y%m%d%H%M%S", localtime; # e.g. temp_20150402102622
   my $staging_directory = join('/', ($self->base_directory, 'staging', $temp_folder));
   try {
     $self->_download_to_staging($species_to_exclude,
                                 $paths_to_database_updates,
                                 $staging_directory);
   } catch {