From 3324da16364de3f5fc38d09d562b95706048df71 Mon Sep 17 00:00:00 2001
From: Dan Staines <dstaines@ebi.ac.uk>
Date: Thu, 10 Oct 2013 09:02:25 +0000
Subject: [PATCH] ran perltidy before making functional changes
---
modules/Bio/EnsEMBL/Utils/CliHelper.pm | 220 ++++++++++++-------------
1 file changed, 110 insertions(+), 110 deletions(-)
diff --git a/modules/Bio/EnsEMBL/Utils/CliHelper.pm b/modules/Bio/EnsEMBL/Utils/CliHelper.pm
index 6249b8267e..9f9cdc5bfc 100644
--- a/modules/Bio/EnsEMBL/Utils/CliHelper.pm
+++ b/modules/Bio/EnsEMBL/Utils/CliHelper.pm
@@ -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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