From 40663f1e1a95467ab1900a338ccf1d00e3720d5b Mon Sep 17 00:00:00 2001
From: Andrew Yates <ayates@ebi.ac.uk>
Date: Mon, 14 May 2012 16:41:36 +0000
Subject: [PATCH] More warnings when we fail to load DBs & the VERBOSE flag is
on
---
modules/Bio/EnsEMBL/Registry.pm | 18 +++++++++++++++++-
1 file changed, 17 insertions(+), 1 deletion(-)
diff --git a/modules/Bio/EnsEMBL/Registry.pm b/modules/Bio/EnsEMBL/Registry.pm
index 9a05d99cd4..26d37dbdcc 100644
--- a/modules/Bio/EnsEMBL/Registry.pm
+++ b/modules/Bio/EnsEMBL/Registry.pm
@@ -1656,6 +1656,7 @@ sub load_registry_from_db {
}
# Register Core like databases
+ my $core_like_dbs_found = 0;
foreach my $type (qw(core cdna vega vega_update otherfeatures rnaseq)) {
my @dbs = grep { /^[a-z]+_[a-z0-9]+(?:_[a-z0-9]+)? # species name
@@ -1667,6 +1668,10 @@ sub load_registry_from_db {
_
/x } @dbnames;
+ if(@dbs) {
+ $core_like_dbs_found = 1;
+ }
+
foreach my $database (@dbs) {
if ( index( $database, 'collection' ) != -1 ) {
# Skip multi-species databases.
@@ -1685,7 +1690,7 @@ sub load_registry_from_db {
/x );
if(!defined($species)){
- warn "for $database cannot get species??\n";
+ warn "Cannot extract species name from database '$database'";
}
my $dba =
@@ -1745,6 +1750,9 @@ sub load_registry_from_db {
}
} ## end foreach my $multidb (@multi_dbs)
+ if(!$core_like_dbs_found && $verbose) {
+ print("No core-like databases found. Check your DB_VERSION (used '$software_version')\n");
+ }
# User upload DBs
@@ -1825,6 +1833,10 @@ sub load_registry_from_db {
my @variation_dbs =
grep { /^[a-z]+_[a-z0-9]+(?:_[a-z0-9]+)?_variation_(?:\d+_)?\d+_/ } @dbnames;
+ if(! @variation_dbs && $verbose) {
+ print("No variation databases found\n");
+ }
+
for my $variation_db (@variation_dbs) {
if ( index( $variation_db, 'collection' ) != -1 ) {
@@ -1901,6 +1913,10 @@ sub load_registry_from_db {
} else {
my @funcgen_dbs =
grep { /^[a-z]+_[a-z0-9]+(?:_[a-z0-9]+)?_funcgen_(?:\d+_)?\d+_/ } @dbnames;
+
+ if(! @funcgen_dbs && $verbose) {
+ print("No funcgen databases found\n");
+ }
for my $funcgen_db (@funcgen_dbs) {
if ( index( $funcgen_db, 'collection' ) != -1 ) {
--
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