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Commit 3324da16 authored by Dan Staines's avatar Dan Staines
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ran perltidy before making functional changes

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modules/Bio/EnsEMBL/Utils/CliHelper.pm
+ 110
− 110
View file @ 3324da16
......@@ -86,17 +86,15 @@ 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' },
];
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()
......@@ -107,9 +105,9 @@ my $dba_opts =
=cut
sub new {
my ( $class, @args ) = @_;
my $self = bless( {}, ref($class) || $class );
return $self;
my ( $class, @args ) = @_;
my $self = bless( {}, ref($class) || $class );
return $self;
}
=head2 get_dba_opts()
......@@ -122,13 +120,13 @@ sub new {
=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;
my ( $self, $prefix ) = @_;
$prefix ||= '';
my @dba_opts = map {
my $opt = join '|', map { $prefix . $_ } @{ $_->{args} };
$opt . $_->{type};
} @{$dba_opts};
return \@dba_opts;
}
=head2 process_args()
......@@ -142,12 +140,12 @@ sub get_dba_opts {
=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;
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()
......@@ -164,75 +162,77 @@ sub process_args {
=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(
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} ) == 0 ) {
croak "No species.production_name found in database";
}
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';
);
if ( scalar( @{$species_ids} ) == 0 ) {
croak "No species.production_name found in database";
}
return \@db_args;
if ( scalar( @{$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 for my $dbname (@dbnames)
} ## 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()
......@@ -248,16 +248,17 @@ sub get_dba_args_for_opts {
=cut
sub get_dbas_for_opts {
my ( $self, $opts, $single_species, $prefix ) = @_;
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;
my $dbas;
for my $args (
@{ $self->get_dba_args_for_opts( $opts, $single_species, $prefix ) }
)
{
push @{$dbas}, Bio::EnsEMBL::DBSQL::DBAdaptor->new( %{$args} );
}
return $dbas;
}
=head2 load_registry_for_opts
......@@ -274,18 +275,17 @@ sub get_dbas_for_opts {
=cut
sub load_registry_for_opts {
my ($self, $opts, $prefix) = @_;
my ( $self, $opts, $prefix ) = @_;
$prefix ||= q{};
if($opts->{registry}) {
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},
);
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);
}
......
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