diff --git a/modules/Bio/EnsEMBL/AltAlleleGroup.pm b/modules/Bio/EnsEMBL/AltAlleleGroup.pm
index 54b286662d61126cf205897b776b8bac63bfde37..cca48d6c7335ca5badea43cd059f844cf77a101e 100644
--- a/modules/Bio/EnsEMBL/AltAlleleGroup.pm
+++ b/modules/Bio/EnsEMBL/AltAlleleGroup.pm
@@ -224,7 +224,8 @@ sub rep_Gene_id {
$self->{'MEMBERS'} = $list;
return $new_id;
} elsif ($new_id && !$change) {
- throw("Requested representative gene ID was not set because it is not in this AltAlleleGroup, ID ".$self->dbID);
+ my $db_id = $self->dbID() || 'unknown';
+ throw("Requested representative gene ID was not set because it is not in this AltAlleleGroup, ID $db_id");
}
else {
warning("No representative allele currently set for this AltAlleleGroup");
diff --git a/modules/t/MultiTestDB.conf.default b/modules/t/MultiTestDB.conf.default
index c3bc1fde9c0b0d7c641d0e5fb4e0cbea72c5c479..cbf5fbda54854b12a19c6e838ea9f736b8ea4c2a 100644
--- a/modules/t/MultiTestDB.conf.default
+++ b/modules/t/MultiTestDB.conf.default
@@ -9,6 +9,7 @@
'core' => 'Bio::EnsEMBL::DBSQL::DBAdaptor',
'patch' => 'Bio::EnsEMBL::DBSQL::DBAdaptor',
'empty' => 'Bio::EnsEMBL::DBSQL::DBAdaptor',
+ 'patch' => 'Bio::EnsEMBL::DBSQL::DBAdaptor',
},
'circ' => {
'core' => 'Bio::EnsEMBL::DBSQL::DBAdaptor',
diff --git a/modules/t/altAlleleGroup.t b/modules/t/altAlleleGroup.t
index 4f364e2bbb19c04242ff187cfc3580f6fb83050e..416bcbd938edf204a98fa03a9bbee473904e7eb2 100644
--- a/modules/t/altAlleleGroup.t
+++ b/modules/t/altAlleleGroup.t
@@ -36,10 +36,14 @@ is_deeply($id_list,[qw( 1 2 3 )], "Get all Gene IDs within a prefab group");
my $id = $group->rep_Gene_id();
is($id,'2',"Get reference Gene ID");
-is($other_group->rep_Gene_id(),undef,"Test behaviour without a reference Gene set");
+warns_like {
+ is($other_group->rep_Gene_id(),undef,"Test behaviour without a reference Gene set");
+} qr/No representative allele currently set/, 'Ensuring appropriate warning about lack of reference gene is emitted';
$group->unset_rep_Gene_id();
-is($group->rep_Gene_id(), undef,"Check successful unsetting.");
+warns_like {
+ is($group->rep_Gene_id(), undef,"Check successful unsetting.");
+} qr/No representative allele currently set/, 'Ensuring appropriate warning about lack of reference gene is emitted';
throws_ok{$group->rep_Gene_id(5)} qr/Requested representative gene ID/, "Exception thrown when invalid ID given";
ok($group->rep_Gene_id(3) == 3,"Successful setting of reference gene");
diff --git a/modules/t/dbEntries.t b/modules/t/dbEntries.t
index f74400887edcec8ae3c0a2a14fcee13af125c9a5..77c2738922709f0c8f6780dce2291f0d4b0e3467 100644
--- a/modules/t/dbEntries.t
+++ b/modules/t/dbEntries.t
@@ -199,44 +199,44 @@ $xref = Bio::EnsEMBL::DBEntry->new
);
my $threaded;
- use Config;
- if($Config{useithreads}) {
- note 'Using threaded tests';
- require threads;
- $threaded = 1;
- {
- local $ENV{RUNTESTS_HARNESS} = 1;
- local $ENV{RUNTESTS_HARNESS_NORESTORE} = 1;
-
- # db connection must be severed for threads to access DB
- $dbEntryAdaptor->dbc->disconnect_if_idle();
- $multi->get_DBAdaptor('empty'); # seem to have to do this to stop thread whinging under some perls
-
- my $parallel_store = sub{
- my $xref_id = $dbEntryAdaptor->store( $xref, $tr->dbID, "Transcript" );
- return $xref_id
- };
-
- my $thread1 = threads->create($parallel_store);
- my $thread2 = threads->create($parallel_store);
- my $thread3 = threads->create($parallel_store);
-
-
- my @xref_ids;
- @xref_ids = ($thread1->join,$thread2->join,$thread3->join);
-
- note("Threaded xrefs: ".$xref_ids[0]." ".$xref_ids[1]." ".$xref_ids[2]);
-
- # Test 10 - Verify that only one xref has been inserted under parallel inserts
- is($xref_ids[0], 1000009, 'Thread 1 ID assertion');
- is($xref_ids[1], $xref_ids[0], 'Thread 2 ID is the same as thread 1');
- is($xref_ids[2], $xref_ids[0], 'Thread 3 ID is the same as thread 1');
- }
-
- }
- else {
- note 'Skipping threaded tests';
+use Config;
+if($Config{useithreads}) {
+ note 'Using threaded tests';
+ require threads;
+ $threaded = 1;
+ {
+ local $ENV{RUNTESTS_HARNESS} = 1;
+ local $ENV{RUNTESTS_HARNESS_NORESTORE} = 1;
+
+ # db connection must be severed for threads to access DB
+ $dbEntryAdaptor->dbc->disconnect_if_idle();
+ $multi->get_DBAdaptor('empty'); # seem to have to do this to stop thread whinging under some perls
+
+ my $parallel_store = sub{
+ my $xref_id = $dbEntryAdaptor->store( $xref, $tr->dbID, "Transcript" );
+ return $xref_id
+ };
+
+ my $thread1 = threads->create($parallel_store);
+ my $thread2 = threads->create($parallel_store);
+ my $thread3 = threads->create($parallel_store);
+
+
+ my @xref_ids;
+ @xref_ids = ($thread1->join,$thread2->join,$thread3->join);
+
+ note("Threaded xrefs: ".$xref_ids[0]." ".$xref_ids[1]." ".$xref_ids[2]);
+
+ # Test 10 - Verify that only one xref has been inserted under parallel inserts
+ is($xref_ids[0], 1000003, 'Thread 1 ID assertion');
+ is($xref_ids[1], $xref_ids[0], 'Thread 2 ID is the same as thread 1');
+ is($xref_ids[2], $xref_ids[0], 'Thread 3 ID is the same as thread 1');
}
+
+}
+else {
+ note 'Skipping threaded tests';
+}
# Test 11 - Exception testing on ->store()
@@ -260,9 +260,9 @@ $xref = Bio::EnsEMBL::DBEntry->new
my $xref_id = $dbEntryAdaptor->store($xref, undef, "Transcript");
note("Xref_id from insert: ".$xref_id);
if ($threaded) {
- ok($xref_id == 1000010);
+ ok($xref_id == 1000004);
} else {
- is($xref_id,1000009, "dbID for new DBEntry.");
+ is($xref_id,1000003, "dbID for new DBEntry.");
}
#
diff --git a/modules/t/gene.t b/modules/t/gene.t
index 010dc2fd18877de386a51a9c3bc3ebd6b124322b..5ae01f58cd2c841a4e0e45a0c0177eff55b7f5cb 100644
--- a/modules/t/gene.t
+++ b/modules/t/gene.t
@@ -544,15 +544,16 @@ push(@alt_genes, $ga->fetch_by_dbID(18270));
push(@alt_genes, $ga->fetch_by_dbID(18271));
push(@alt_genes, $ga->fetch_by_dbID(18272));
-warns_like(
- sub {
-# my ($stdout_ref, $stderr_ref) = @_;
- $ga->store_alt_alleles(\@alt_genes);
-# my $check = qr/.+alternative.+reference\ssequence.+Ignoring/;
-# like(${$stderr_ref}, $check, 'Checking we are still warning about multiple alt_alleles on refs');
- }, qr/.+alternative.+reference\ssequence.+Ignoring/, 'Checking we are still warning about multiple alt_alleles on refs');
+warns_like {
+ $ga->store_alt_alleles(\@alt_genes);
+} qr/.+alternative.+reference\ssequence.+Ignoring/, 'Checking we are still warning about multiple alt_alleles on refs';
$gene = $ga->fetch_by_dbID(18270);
-$alt_genes = $gene->get_all_alt_alleles();
+
+note 'Do not use GeneAdaptor::store_alt_alleles() for storing alt alleles. Ensuring we still warn';
+warns_like {
+ $alt_genes = $gene->get_all_alt_alleles();
+} qr/Supplied gene has no alternative alleles/, 'Passing multiple genes to GeneAdaptor::store_alt_alleles() results in no REF being stored';
+
%gene_ids = (18271 => 1, 18272 => 1);
$ok = 1;