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

package Bio::VertRes::Config::Pipelines::Common;

# ABSTRACT: A set of attributes common to all pipeline config files


use Moose;
use File::Slurp;
use Bio::VertRes::Config::Types;
use Data::Dumper;
use File::Basename;
use File::Path qw(make_path);
with 'Bio::VertRes::Config::Pipelines::Roles::RootDatabaseLookup';

has 'prefix'              => ( is => 'ro', isa => 'Bio::VertRes::Config::Prefix', default  => '_' );
has 'pipeline_short_name' => ( is => 'ro', isa => 'Str',                          required => 1 );
has 'module'              => ( is => 'ro', isa => 'Str',                          required => 1 );
has 'toplevel_action'     => ( is => 'ro', isa => 'Str',                          required => 1 );

has 'overwrite_existing_config_file' => ( is => 'ro', isa => 'Bool', default => 0 );

has 'log' => ( is => 'ro', isa => 'Str', lazy => 1, builder => '_build_log' );
has 'log_base'      => ( is => 'ro', isa => 'Str', required => 1 );
has 'log_file_name' => ( is => 'ro', isa => 'Str', default => 'logfile.log' );

has 'config' => ( is => 'ro', isa => 'Str', lazy => 1, builder => '_build_config' );
has 'config_base'      => ( is => 'ro', isa => 'Str', required => 1 );
has 'config_file_name' => ( is => 'ro', isa => 'Str', default  => 'global.conf' );

has 'root' => ( is => 'ro', isa => 'Str', lazy => 1, builder => '_build_root' );
has 'root_base'            => ( is => 'ro', isa => 'Str', required => 1 );
has 'root_pipeline_suffix' => ( is => 'ro', isa => 'Str', default => 'seq-pipelines' );

has 'database' => ( is => 'ro', isa => 'Str',        required => 1 );
has 'host'     => ( is => 'ro', isa => 'Str',        lazy     => 1, builder => '_build_host' );
has 'port'     => ( is => 'ro', isa => 'Int',        lazy     => 1, builder => '_build_port' );
has 'user'     => ( is => 'ro', isa => 'Str',        lazy     => 1, builder => '_build_user' );
has 'password' => ( is => 'ro', isa => 'Maybe[Str]', lazy     => 1, builder => '_build_password' );

has 'database_connect_file' => ( is => 'ro', isa => 'Str', required => 1 );
has '_database_connection_details' =>
  ( is => 'ro', isa => 'Maybe[HashRef]', lazy => 1, builder => '_build__database_connection_details' );

sub _build_root {
    my ($self) = @_;
    join( '/', ( $self->root_base, $self->root_database_name, $self->root_pipeline_suffix ) );
}

sub _build_config {
    my ($self) = @_;
    my $conf_file_name = join( '_', ( $self->pipeline_short_name, $self->config_file_name ) );
    join( '/', ( $self->config_base, $self->root_database_name, $self->pipeline_short_name, $conf_file_name ) );
}

sub _build_log {
    my ($self) = @_;
    my $log_file_name = join( '_', ( $self->pipeline_short_name, $self->log_file_name ) );
    join( '/', ( $self->log_base, $self->root_database_name, $log_file_name ) );
}

sub _build_host {
    my ($self) = @_;
    if ( defined( $self->_database_connection_details ) ) {
        return $self->_database_connection_details->{host};
    }
    return $ENV{VRTRACK_HOST} || 'localhost';
}

sub _build_port {
    my ($self) = @_;
    if ( defined( $self->_database_connection_details ) ) {
        return $self->_database_connection_details->{port};
    }
    return $ENV{VRTRACK_PORT} || 3306;
}

sub _build_user {
    my ($self) = @_;
    if ( defined( $self->_database_connection_details ) ) {
        return $self->_database_connection_details->{user};
    }
    return $ENV{VRTRACK_RW_USER} || 'root';
}

sub _build_password {
    my ($self) = @_;
    if ( defined( $self->_database_connection_details ) ) {
        return $self->_database_connection_details->{password};
    }
    return $ENV{VRTRACK_PASSWORD};
}

sub _build__database_connection_details {
    my ($self) = @_;
    my $connection_details;
    if ( -f $self->database_connect_file ) {
        my $text = read_file( $self->database_connect_file );
        $connection_details = eval($text);
    }
    return $connection_details;
}