Bio-VertRes-Config

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

use Moose;
use Bio::VertRes::Config::RegisterStudy;
with 'Bio::VertRes::Config::Pipelines::Roles::RootDatabaseLookup';

has 'default_database_name' => ( is => 'ro', isa => 'Str', required => 1 );
has 'study_name'            => ( is => 'ro', isa => 'Str', required => 1 );
has 'config_base'           => ( is => 'ro', isa => 'Str', required => 1 );

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

    # In the normal case the study will be in the default database, so check it first to save on IO
    if (
        Bio::VertRes::Config::RegisterStudy->new(
            database    => $self->default_database_name,
            study_name  => $self->study_name,
            config_base => $self->config_base
        )->is_study_in_file_already == 1
      )

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

=head1 SYNOPSIS

Prevent a study name from being registered in two different databases.
   use Bio::VertRes::Config::CommandLine::StudyNameSearch;

   my $obj = Bio::VertRes::Config::CommandLine::StudyNameSearch->new(
     default_database_name => 'pathogen_rnd_track', 
     config_base => $destination_directory,
     study_name => 'Unseen study'
     );
   $obj->get_study_database_name_or_default_if_not_found;

=head1 METHODS

=head2 get_study_database_name_or_default_if_not_found

Lookup the study name in all the standard databases. If its found then return that database. If its a new study return the default.

=head1 AUTHOR

Andrew J. Page <ap13@sanger.ac.uk>

=head1 COPYRIGHT AND LICENSE

This software is Copyright (c) 2013 by Wellcome Trust Sanger Institute.

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

  my ($self) = @_;
  
  if(defined($self->limits->{project}))
  {
    for my $study_name ( @{$self->limits->{project}} )
    {
      $self->database(Bio::VertRes::Config::CommandLine::StudyNameSearch->new(
        default_database_name => $self->database, 
        config_base => $self->config_base,
        study_name => $study_name,
        )->get_study_database_name_or_default_if_not_found);
    }
  }
};


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

    my $top_level = Bio::VertRes::Config::MultipleTopLevelFiles->new(
        database            => $self->database,

t/Bio/VertRes/Config/CommandLine/StudyNameSearch.t  view on Meta::CPAN

Bio::VertRes::Config::RegisterStudy->new(database => 'pathogen_rnd_track', study_name => 'EFG study',config_base => $destination_directory)->register_study_name();
Bio::VertRes::Config::RegisterStudy->new(database => 'pathogen_prok_track', study_name => 'CCC',config_base => $destination_directory)->register_study_name();
Bio::VertRes::Config::RegisterStudy->new(database => 'pathogen_euk_track', study_name => 'DDD',config_base => $destination_directory)->register_study_name();


ok(my $obj = Bio::VertRes::Config::CommandLine::StudyNameSearch->new(
  default_database_name => 'pathogen_rnd_track', 
  config_base => $destination_directory,
  study_name => 'Unseen study'
  ), 'Initialise object for unseen study');
is($obj->get_study_database_name_or_default_if_not_found, 'pathogen_rnd_track', 'unseen study returns default database');

ok($obj = Bio::VertRes::Config::CommandLine::StudyNameSearch->new(
  default_database_name => 'pathogen_rnd_track', 
  config_base => $destination_directory,
  study_name => 'ABC study'
  ), 'Initialise object for seen study in default database');
is($obj->get_study_database_name_or_default_if_not_found, 'pathogen_rnd_track', 'seen study in default database should return default');

ok($obj = Bio::VertRes::Config::CommandLine::StudyNameSearch->new(
  default_database_name => 'pathogen_prok_track', 
  config_base => $destination_directory,
  study_name => 'EFG study'
  ), 'Initialise object for seen study in different database');
is($obj->get_study_database_name_or_default_if_not_found, 'pathogen_rnd_track', 'find study in another database');


done_testing();