Bio-VertRes-Config

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

# ABSTRACT: Create config scripts


use Moose;
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' );
has 'log_base'    => ( is => 'rw', isa => 'Str', default => '/nfs/pathnfs05/log' );
has 'database_connect_file' =>
  ( is => 'rw', isa => 'Str', default => '/software/pathogen/config/database_connection_details' );
has 'reference_lookup_file' =>
  ( is => 'rw', isa => 'Str', default => '/lustre/scratch108/pathogen/pathpipe/refs/refs.index' );

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

package Bio::VertRes::Config::CommandLine::LogParameters;

# ABSTRACT: A class to represent multiple top level files. It splits out mixed config files into the correct top level files


use Moose;
use Bio::VertRes::Config::Exceptions;
use File::Basename;
use File::Path qw(make_path);

has 'args'           => ( is => 'ro', isa => 'ArrayRef', required => 1 );
has 'script_name'    => ( is => 'ro', isa => 'Str',      required => 1 );
has 'log_file'       => ( is => 'rw', isa => 'Str',      default  => '/tmp/command_line.log' );
has '_output_string' => ( is => 'ro', isa => 'Str',      lazy     => 1, builder => '_build__output_string' );
has '_user_name'     => ( is => 'ro', isa => 'Str',      lazy     => 1, builder => '_build__user_name' );

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

    # Build the variable just after object construction because the array ref gets modified by GetOpts
    $self->_output_string;

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

package Bio::VertRes::Config::MultipleTopLevelFiles;

# ABSTRACT: A class to represent multiple top level files. It splits out mixed config files into the correct top level files


use Moose;
use Bio::VertRes::Config::TopLevel;

has 'database'         => ( is => 'ro', isa => 'Str',      required => 1 );
has 'pipeline_configs' => ( is => 'ro', isa => 'ArrayRef', required => 1 );
has 'config_base'  => ( is => 'ro', isa => 'Str',     required => 1 );

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

    my %short_name_to_configs;

    # split by short name
    for my $pipeline_config ( @{ $self->pipeline_configs } ) {
        # Create the config file

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

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 ) );

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

package Bio::VertRes::Config::Pipelines::Roles::MetaDataFilter;
# ABSTRACT: Moose Role for dealing with limits meta data filters


use Moose::Role;

has 'limits'             => ( is => 'ro', isa => 'HashRef', required => 1 );
has '_escaped_limits'    => ( is => 'ro', isa => 'HashRef', lazy    => 1, builder => '_build__escaped_limits' );

sub _build__escaped_limits
{
  my ($self) = @_;
  my %escaped_limits;
  
  for my $limit_type (keys %{$self->limits}) 
  {
    my @escaped_array_values;
    for my $array_value ( @{$self->limits->{$limit_type}})

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

package Bio::VertRes::Config::Pipelines::Roles::RootDatabaseLookup;

# ABSTRACT: Moose Role for translating non standard database names to their area


use Moose::Role;

has 'root_database_name'     => ( is => 'ro', isa => 'Str',     lazy => 1, builder => '_build_root_database_name' );
has 'non_standard_databases' => ( is => 'ro', isa => 'HashRef', lazy => 1, builder => '_build_non_standard_databases' );

sub _build_root_database_name {
    my ($self) = @_;
    return $self->root_database_name_lookup( $self->database );
}

sub _build_non_standard_databases {
    my ($self) = @_;
    my %non_standard_databases = (
        'pathogen_virus_track'    => 'viruses',

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

use Moose;
use Bio::VertRes::Config::MultipleTopLevelFiles;
use Bio::VertRes::Config::CommandLine::StudyNameSearch;

has 'database'                       => ( is => 'rw', isa => 'Str',  required => 1 );
has 'database_connect_file'          => ( is => 'ro', isa => 'Str',  default => '/software/pathogen/config/database_connection_details' );
has 'config_base'                    => ( is => 'ro', isa => 'Str',  default  => '/nfs/pathnfs05/conf' );
has 'root_base'                      => ( is => 'ro', isa => 'Str',  default  => '/lustre/scratch108/pathogen/pathpipe' );
has 'log_base'                       => ( is => 'ro', isa => 'Str',  default  => '/nfs/pathnfs05/log' );
has 'overwrite_existing_config_file' => ( is => 'ro', isa => 'Bool', default  => 0 );
has 'limits'                         => ( is => 'ro', isa => 'HashRef', default => sub { {} });

has '_pipeline_configs'              => ( is => 'ro', isa => 'ArrayRef', default => sub { [] });


before 'create' => sub { 
  my ($self) = @_;
  
  if(defined($self->limits->{project}))
  {
    for my $study_name ( @{$self->limits->{project}} )
    {
      $self->database(Bio::VertRes::Config::CommandLine::StudyNameSearch->new(

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

package Bio::VertRes::Config::References;

# ABSTRACT: A class for translating between a reference name and the location on disk


use Moose;
use Bio::VertRes::Config::Types;
use Bio::VertRes::Config::Exceptions;

has 'reference_lookup_file'      => ( is => 'ro', isa => 'Bio::VertRes::Config::File', required => 1 );
has '_reference_names_to_files'  => ( is => 'ro', isa => 'HashRef', lazy => 1, builder => '_build__reference_names_to_files');
has 'available_references'  => ( is => 'ro', isa => 'ArrayRef', lazy => 1, builder => '_build_available_references');

sub _build__reference_names_to_files
{
  my ($self) = @_;
  my %reference_names_to_files;
  open(my $index_file, $self->reference_lookup_file) or Bio::VertRes::Config::Exceptions::FileDoesntExist->throw(error => 'Couldnt open file '.$self->reference_lookup_file);
  while(<$index_file>)
  {
    chomp;
    my $line = $_;

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

use Moose;
use File::Basename;
use File::Path qw(make_path);
use Bio::VertRes::Config::Exceptions;
with 'Bio::VertRes::Config::Pipelines::Roles::RootDatabaseLookup';

has 'pipeline_short_name' => ( is => 'ro', isa => 'Str', required => 1 );
has 'database'            => ( is => 'ro', isa => 'Str', required => 1 );
has 'pipeline_configs'    => ( is => 'ro', isa => 'ArrayRef', required => 1 );

has 'overall_config'                   => ( is => 'ro', isa => 'Str',     lazy    => 1, builder => '_build_overall_config' );
has 'config_base'              => ( is => 'ro', isa => 'Str',     required => 1 );
has 'overall_config_file_name'         => ( is => 'ro', isa => 'Str',     lazy    => 1, builder => '_build_overall_config_file_name' );
has '_overall_config_file_name_suffix' => ( is => 'ro', isa => 'Str',     default => 'pipeline.conf' );
has '_filenames_to_action'             => ( is => 'ro', isa => 'HashRef', lazy    => 1, builder => '_build__filenames_to_action' );

has '_filenames_to_action'             => ( is => 'ro', isa => 'HashRef', lazy    => 1, builder => '_build__filenames_to_action' );

sub _build_overall_config_file_name {
    my ($self) = @_;
    return join( '_', ( $self->root_database_name, $self->pipeline_short_name, 'pipeline.conf' ) );
}

sub _build_overall_config {
    my ($self) = @_;
    return join( '/', ( $self->config_base, $self->root_database_name, $self->overall_config_file_name ) );
}