Commit 6ea4ca0a authored by Andy Yates's avatar Andy Yates
Browse files

Undefined value warnings on $species_suffix usage and lowercasing input to...

Undefined value warnings on $species_suffix usage and lowercasing input to allow for matching on registry stored aliases
parent 4abc4693
...@@ -563,7 +563,7 @@ sub add_DBAdaptor { ...@@ -563,7 +563,7 @@ sub add_DBAdaptor {
sub get_DBAdaptor { sub get_DBAdaptor {
my ( $class, $species, $group ) = @_; my ( $class, $species, $group ) = @_;
throw 'arrggh for '.$species if ! defined $species;
$species = $class->get_alias($species); $species = $class->get_alias($species);
return $registry_register{_SPECIES}{$species}{ lc($group) }{'_DB'}; return $registry_register{_SPECIES}{$species}{ lc($group) }{'_DB'};
...@@ -2006,6 +2006,9 @@ sub find_and_add_aliases { ...@@ -2006,6 +2006,9 @@ sub find_and_add_aliases {
my ( $adaptor, $group, $dbh, $species_suffix ) = my ( $adaptor, $group, $dbh, $species_suffix ) =
rearrange( [ 'ADAPTOR', 'GROUP', 'HANDLE', 'SPECIES_SUFFIX' ], @_ ); rearrange( [ 'ADAPTOR', 'GROUP', 'HANDLE', 'SPECIES_SUFFIX' ], @_ );
#Can be undef; needs to be something to avoid warnings
$species_suffix ||= q{};
my @dbas; my @dbas;
if ( defined($adaptor) ) { if ( defined($adaptor) ) {
...@@ -2071,18 +2074,22 @@ sub find_and_add_aliases { ...@@ -2071,18 +2074,22 @@ sub find_and_add_aliases {
} }
foreach my $alias (@aliases) { foreach my $alias (@aliases) {
if ( !$class->alias_exists( $alias . $species_suffix ) my $alias_suffix = $alias.$species_suffix;
&& $species ne $alias . $species_suffix ) #Lowercase because stored aliases are lowercased
my $lc_species = lc($species);
my $lc_alias_suffix = lc($alias_suffix);
if ( !$class->alias_exists( $alias_suffix )
&& $lc_species ne $lc_alias_suffix )
{ {
$class->add_alias( $species, $alias . $species_suffix ); $class->add_alias( $species, $alias_suffix );
} elsif ( } elsif (
$species ne $class->get_alias( $alias . $species_suffix ) ) $lc_species ne $class->get_alias( $alias_suffix ) )
{ {
throw(sprintf( throw(sprintf(
"Trying to add alias '%s' to species '%s', " "Trying to add alias '%s' to species '%s', "
. " but it is already registrered for species '%s'\n", . " but it is already registrered for species '%s'\n",
$alias . $species_suffix, $alias_suffix,
$species, $class->get_alias( $alias . $species_suffix ) $species, $class->get_alias( $alias_suffix )
) ); ) );
} }
} }
......
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