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Commit be644987 authored by Andy Yates's avatar Andy Yates
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[ENSCORESW-710]. Perform alias addition only if we found the DB.

Patch submitted by Yuri Delia as aliases were added into the registry
even if a database was not found e.g. ontology. Additions moved
into the if blocks when we find and DB and constructed its adaptor.
parent e05003a3
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...@@ -2065,6 +2065,11 @@ sub load_registry_from_db { ...@@ -2065,6 +2065,11 @@ sub load_registry_from_db {
} }
} ## end foreach my $compara_db (@compara_dbs) } ## end foreach my $compara_db (@compara_dbs)
} ## end else [ if ($@) } ## end else [ if ($@)
Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
-species => 'multi'.$species_suffix,
-alias => ['compara'.$species_suffix] );
} elsif ($verbose) { } elsif ($verbose) {
print("No Compara databases found\n"); print("No Compara databases found\n");
} }
...@@ -2100,6 +2105,11 @@ sub load_registry_from_db { ...@@ -2100,6 +2105,11 @@ sub load_registry_from_db {
join( ', ', @ancestral_dbs ) ); join( ', ', @ancestral_dbs ) );
} }
} }
Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
-species => 'Ancestral sequences'.$species_suffix,
-alias => ['ancestral_sequences'.$species_suffix] );
} elsif ($verbose) { } elsif ($verbose) {
print("No ancestral database found\n"); print("No ancestral database found\n");
} }
...@@ -2122,6 +2132,11 @@ sub load_registry_from_db { ...@@ -2122,6 +2132,11 @@ sub load_registry_from_db {
if ($verbose) { if ($verbose) {
printf( "%s loaded\n", $ontology_db ); printf( "%s loaded\n", $ontology_db );
} }
Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
-species => 'multi'.$species_suffix,
-alias => ['ontology'.$species_suffix] );
} }
elsif ($verbose) { elsif ($verbose) {
print("No ontology database found\n"); print("No ontology database found\n");
...@@ -2144,25 +2159,11 @@ sub load_registry_from_db { ...@@ -2144,25 +2159,11 @@ sub load_registry_from_db {
printf( "%s loaded\n", $stable_ids_db ); printf( "%s loaded\n", $stable_ids_db );
} }
} Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
-species => 'multi'.$species_suffix,
-alias => ['stable_ids'.$species_suffix] );
}
Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
-species => 'multi'.$species_suffix,
-alias => ['compara'.$species_suffix] );
Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
-species => 'multi'.$species_suffix,
-alias => ['ontology'.$species_suffix] );
Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
-species => 'multi'.$species_suffix,
-alias => ['stable_ids'.$species_suffix] );
Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
-species => 'Ancestral sequences'.$species_suffix,
-alias => ['ancestral_sequences'.$species_suffix] );
# Register aliases as found in adaptor meta tables. # Register aliases as found in adaptor meta tables.
......
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