view variant_effect_predictor/Bio/EnsEMBL/Utils/CliHelper.pm @ 3:d30fa12e4cc5 default tip

Merge heads 2:a5976b2dce6f and 1:09613ce8151e which were created as a result of a recently fixed bug.

=head1 LICENSE

  Copyright (c) 1999-2012 The European Bioinformatics Institute and
  Genome Research Limited.  All rights reserved.

  This software is distributed under a modified Apache license.
  For license details, please see

    http://www.ensembl.org/info/about/code_licence.html

=head1 CONTACT

  Please email comments or questions to the public Ensembl
  developers list at <[e-mail]>.

  Questions may also be sent to the Ensembl help desk at
  <[e-mail]>.

=cut

=head1 NAME

Bio::EnsEMBL::Utils::CliHelper

=head1 VERSION

$Revision: 1.6 $

=head1 SYNOPSIS

  use Bio::EnsEMBL::Utils::CliHelper;

  my $cli = Bio::EnsEMBL::Utils::CliHelper->new();

  # get the basic options for connecting to a database server
  my $optsd = $cli->get_dba_opts();

  # add the print option
  push(@$optsd,"print|p");

  # process the command line with the supplied options plus a reference to a help subroutine
  my $opts = $cli->process_args($optsd,\&usage);
  
  # use the command line options to get an array of database details
  for my $db_args (@{$cli->get_dba_args_for_opts($opts)}) {
    # use the args to create a DBA
    my $dba = new Bio::EnsEMBL::DBSQL::DBAdaptor(%{$db_args});
    ...
  }
  
  For adding secondary databases, a prefix can be supplied. For instance, to add a second set of
  db params prefixed with dna (-dnahost -dbport etc.) use the prefix argument with get_dba_opts and 
  get_dba_args_for_opts:
  # get the basic options for connecting to a database server
  my $optsd =
   [ @{ $cli_helper->get_dba_opts() }, @{ $cli_helper->get_dba_opts('gc') } ];
  # process the command line with the supplied options plus a help subroutine
  my $opts = $cli_helper->process_args( $optsd, \&usage );
  # get the dna details
  my ($dna_dba_details) =
    @{ $cli_helper->get_dba_args_for_opts( $opts, 1, 'dna' ) };
  my $dna_db =
    Bio::EnsEMBL::DBSQL::DBAdaptor->new( %{$dna_dba_details} ) );

=head1 DESCRIPTION

Utilities for a more consistent approach to parsing and handling EnsEMBL script command lines

=head1 METHODS

See subroutines.

=cut

package Bio::EnsEMBL::Utils::CliHelper;

use warnings;
use strict;

use Carp;
use Data::Dumper;
use Getopt::Long qw(:config auto_version no_ignore_case);

use Bio::EnsEMBL::Registry;
use Bio::EnsEMBL::DBSQL::DBConnection;
use Bio::EnsEMBL::DBSQL::DBAdaptor;

my $dba_opts =
  [ { args => [ 'host', 'dbhost', 'h'  ], type => '=s' },
    { args => [ 'port', 'dbport', 'P'  ], type => ':i' },
    { args => [ 'user', 'dbuser', 'u'  ], type => '=s' },
    { args => [ 'pass', 'dbpass', 'p'  ], type => ':s' },
    { args => [         'dbname', 'D'  ], type => ':s' },
    { args => [ 'pattern', 'dbpattern' ], type => ':s' },
    { args => [ 'driver'               ], type => ':s' },
    { args => [ 'species_id'           ], type => ':i' },
    { args => [ 'species'              ], type => ':i' },
  ];

=head2 new()

  Description : Construct a new instance of a CliHelper object
  Returntype  : Bio::EnsEMBL::Utils:CliHelper
  Status      : Under development

=cut

sub new {
	my ( $class, @args ) = @_;
	my $self = bless( {}, ref($class) || $class );
	return $self;
}

=head2 get_dba_opts()

  Arg [1]     : Optional prefix for dbnames e.g. dna
  Description : Retrieves the standard options for connecting to one or more Ensembl databases
  Returntype  : Arrayref of option definitions
  Status      : Under development

=cut

sub get_dba_opts {
	my ( $self, $prefix ) = @_;
	$prefix ||= '';
	my @dba_opts = map {
		my $opt = join '|', map { $prefix . $_ } @{ $_->{args} };
		$opt . $_->{type};
	} @{$dba_opts};
	return \@dba_opts;
}

=head2 process_args()

    Arg [1]     : Arrayref of supported command line options (e.g. from get_dba_opts)
    Arg [2]     : Ref to subroutine to be invoked when -help or -? is supplied
    Description : Retrieves the standard options for connecting to one or more Ensembl databases
    Returntype  : Hashref of parsed options
    Status      : Under development

=cut

sub process_args {
	my ( $self, $opts_def, $usage_sub ) = @_;
	my $opts = {};
	push @{$opts_def}, q/help|?/ => $usage_sub;
	GetOptions( $opts, @{$opts_def} )
	  || croak 'Could not parse command line arguments';
	return $opts;
}

=head2 get_dba_args_for_opts()

    Arg [1]     : Hash of options (e.g. parsed from command line options by process_args())
    Arg [2]     : If set to 1, the databases are assumed to have a single species only. Default is 0.
    Arg [3]     : Optional prefix to use when parsing e.g. dna
    Description : Uses the parsed command line options to generate an array of DBAdaptor arguments 
                : (e.g. expands dbpattern, finds all species_ids for multispecies databases)
                : These can then be passed directly to Bio::EnsEMBL::DBSQL::DBAdaptor->new()
    Returntype  : Arrayref of DBA argument hash refs 
    Status      : Under development

=cut

sub get_dba_args_for_opts {
	my ( $self, $opts, $single_species, $prefix ) = @_;
	$prefix         ||= '';
	$single_species ||= 0;
	my ( $host, $port, $user, $pass, $dbname, $pattern, $driver ) =
	  map { $prefix . $_ } qw(host port user pass dbname pattern driver);
	my @db_args;
	if ( defined $opts->{$host} ) {
		my $dbc =
		  Bio::EnsEMBL::DBSQL::DBConnection->new( -USER   => $opts->{$user},
                                                          -PASS   => $opts->{$pass},
                                                          -HOST   => $opts->{$host},
                                                          -PORT   => $opts->{$port},
                                                          -DRIVER => $opts->{$driver} );
		my @dbnames;
		if ( defined $opts->{$dbname} ) {
			push @dbnames, $opts->{$dbname};
		} elsif ( defined $opts->{$pattern} ) {
		   # get a basic DBConnection and use to find out which dbs are involved
			@dbnames =
			  grep { m/$opts->{pattern}/smx }
			  @{ $dbc->sql_helper()->execute_simple(q/SHOW DATABASES/) };
		} else {
			print Dumper($opts);
			croak 'dbname or dbpattern arguments required';
		}
		for my $dbname (@dbnames) {

      #Decipher group of DBAdaptor by capturing the name_name(_name?)_core_ code. Otherwise we don't know 
      my ($group) = $dbname =~ /^[a-z]+_[a-z0-9]+(?:_[a-z0-9]+)?_([a-z]+)(?:_\d+)?_\d+/;
            
			my $multi = 0;
			my $species_ids = [ [ 1, undef ] ];
			if ( !$single_species ) {
				$species_ids =
				  $dbc->sql_helper()
				  ->execute(
"SELECT species_id,meta_value FROM $dbname.meta WHERE meta_key='species.production_name'"
				  );
				if ( scalar( @{$species_ids} ) > 1 ) {
					$multi = 1;
				}
				if ( defined $opts->{species_id} ) {
					$species_ids =
					  [ [ $opts->{species_id}, $opts->{species} ] ];
				}
			}
			for my $species_id ( @{$species_ids} ) {
				my $args = {
					-HOST            => $opts->{$host},
					-USER            => $opts->{$user},
					-PORT            => $opts->{$port},
					-PASS            => $opts->{$pass},
					-DBNAME          => $dbname,
					-DRIVER          => $opts->{$driver},
					-SPECIES_ID      => $species_id->[0],
					-SPECIES         => $species_id->[1],
					-MULTISPECIES_DB => $multi };
				$args->{-GROUP} = $group if $group;
				push(@db_args, $args);
			}
		}
	} ## end if ( defined $opts->{$host...})
        else {
            croak '(db)host arguments required';
        }
	return \@db_args;
} ## end sub get_dba_args_for_opts

=head2 get_dba_args_for_opts()

    Arg [1]     : Hash of options (e.g. parsed from command line options by process_args())
    Arg [2]     : If set to 1, the databases are assumed to have a single species only. Default is 0.
    Arg [3]     : Optional prefix to use when parsing e.g. dna
    Description : Uses the parsed command line options to generate an array DBAdaptors. 
                : Note this can overload connections on a server
    Returntype  : Arrayref of Bio::EnsEMBL::DBSQL::DBAdaptor
    Status      : Under development

=cut

sub get_dbas_for_opts {
	my ( $self, $opts, $single_species, $prefix ) = @_;

# get all the DBA details that we want to work with and create DBAs for each in turn
	my $dbas;
	for my $args (
		  @{ $self->get_dba_args_for_opts( $opts, $single_species, $prefix ) } )
	{
		push @{$dbas}, Bio::EnsEMBL::DBSQL::DBAdaptor->new( %{$args} );
	}
	return $dbas;
}

=head2 load_registry_for_opts

  Arg [1]    	: Hash of options (e.g. parsed from command line options by process_args()) 
  Arg [2]     : Optional prefix to use when parsing e.g. dna or master 
  Description	: Loads a Registry from the given options hash. If a C<registry> 
                option is given then the code will call C<load_all>. Otherwise
                we use the database parameters given to call 
                C<load_registry_from_db()>.
  Returntype  : Integer of the number of DBAdaptors loaded
  Status      : Under development

=cut

sub load_registry_for_opts {
  my ($self, $opts, $prefix) = @_;
  $prefix ||= q{};
  if($opts->{registry}) {
    my $location = $opts->{registry};
    return Bio::EnsEMBL::Registry->load_all($location);
  }
  my ( $host, $port, $user, $pass ) = map { $prefix . $_ } qw(host port user pass);
  my %args = (
    -HOST => $opts->{$host},
    -PORT => $opts->{$port},
    -USER => $opts->{$user},
  );
  $args{-PASS} = $opts->{$pass};
  return Bio::EnsEMBL::Registry->load_registry_from_db(%args);
}

1;