From ed319106538a97a7cdf4729fa823560b2c6c00f8 Mon Sep 17 00:00:00 2001
From: Marek Szuba <marek.szuba@ebi.ac.uk>
Date: Thu, 31 Oct 2019 14:24:06 +0000
Subject: [PATCH] Registry: add support for versioned ncbi_taxonomy DBs
See ENSCORESW-3253. If both a versioned and an unversioned database are
present, use the versioned one if the version number matches that of the
software.
---
modules/Bio/EnsEMBL/Registry.pm | 22 +++++++++++++++++++---
1 file changed, 19 insertions(+), 3 deletions(-)
diff --git a/modules/Bio/EnsEMBL/Registry.pm b/modules/Bio/EnsEMBL/Registry.pm
index dc97ac3efd..2ea464296f 100644
--- a/modules/Bio/EnsEMBL/Registry.pm
+++ b/modules/Bio/EnsEMBL/Registry.pm
@@ -1742,6 +1742,7 @@ sub load_registry_from_db {
my $ontology_version;
my $taxonomy_db;
+ my $taxonomy_db_versioned;
my $ensembl_metadata_db;
my $ensembl_metadata_db_versioned;
@@ -1817,6 +1818,11 @@ sub load_registry_from_db {
}
} elsif ( $db =~ /^ncbi_taxonomy$/ ) {
$taxonomy_db = $db;
+ }
+ elsif ( $db =~ m{ \A ncbi_taxonomy_(\d+) \z }msx ) {
+ if ( $1 eq $software_version ) {
+ $taxonomy_db_versioned = $db;
+ }
} elsif ( $db =~ /^ensembl_metadata$/ ) {
$ensembl_metadata_db = $db;
}
@@ -2327,7 +2333,7 @@ sub load_registry_from_db {
# Taxonomy
- if ( defined $taxonomy_db) {
+ if ( ( defined $taxonomy_db ) || ( defined $taxonomy_db_versioned ) ) {
my $has_taxonomy = eval {require Bio::EnsEMBL::Taxonomy::DBSQL::TaxonomyDBAdaptor};
if($@ or (!defined $has_taxonomy)) {
@@ -2335,6 +2341,16 @@ sub load_registry_from_db {
print "ensembl_taxonomy API not found - ignoring $taxonomy_db\n";
}
} else {
+
+ my $taxonomy_dbname;
+ # Versioned database has priority over unversioned one.
+ if ( defined $taxonomy_db_versioned ) {
+ $taxonomy_dbname = $taxonomy_db_versioned;
+ }
+ else {
+ $taxonomy_dbname = $taxonomy_db;
+ }
+
my $dba = Bio::EnsEMBL::Taxonomy::DBSQL::TaxonomyDBAdaptor->new(
'-species' => 'multi' . $species_suffix,
'-group' => 'taxonomy',
@@ -2342,10 +2358,10 @@ sub load_registry_from_db {
'-port' => $port,
'-user' => $user,
'-pass' => $pass,
- '-dbname' => $taxonomy_db, );
+ '-dbname' => $taxonomy_dbname, );
if ($verbose) {
- printf( "%s loaded\n", $taxonomy_db );
+ printf( "%s loaded\n", $taxonomy_dbname );
}
}
}
--
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