From 80e8a271ad2d74057ad749398caab89818a423bd Mon Sep 17 00:00:00 2001
From: Magali Ruffier <mr6@ebi.ac.uk>
Date: Wed, 7 Jan 2015 13:15:52 +0000
Subject: [PATCH] ENSCORESW-1193: added is_empty method to check if there is
genome data available
---
modules/Bio/EnsEMBL/DBSQL/GenomeContainer.pm | 30 ++++++++++++++++++++
modules/t/genomeContainer.t | 8 ++++++
2 files changed, 38 insertions(+)
diff --git a/modules/Bio/EnsEMBL/DBSQL/GenomeContainer.pm b/modules/Bio/EnsEMBL/DBSQL/GenomeContainer.pm
index c49a1c82c8..b68ac21966 100644
--- a/modules/Bio/EnsEMBL/DBSQL/GenomeContainer.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/GenomeContainer.pm
@@ -632,6 +632,36 @@ sub _get_statistic {
return \@results;
}
+=head2 is_empty
+
+ Arg [1] : none
+ Example : $results = $genome->is_empty;
+ Description: Boolean to check if there is data in the genome container
+ Returntype : Boolean
+ Exceptions : none
+ Caller : general
+ Status : Stable
+
+=cut
+
+sub is_empty {
+ my $self = shift;
+ my $db = $self->db;
+ my $species_id = $self->db->species_id();
+ my $is_empty = 0;
+ my $count_sql = q{
+ SELECT count(*) FROM genome_statistics
+ };
+
+ my $sth = $self->prepare($count_sql);
+ $sth->execute();
+ if ($sth->fetchrow()) {
+ $is_empty = 1;
+ }
+ $sth->finish();
+ return $is_empty;
+}
+
=head2 get_attrib
Arg [1] : statistic
diff --git a/modules/t/genomeContainer.t b/modules/t/genomeContainer.t
index d91b0a3c25..87880d49a7 100644
--- a/modules/t/genomeContainer.t
+++ b/modules/t/genomeContainer.t
@@ -173,6 +173,14 @@ is(0, $empty_genome->has_karyotype, "Empty db does not have chromosomes");
is(1, $genome->is_high_coverage, "Human genebuild is high coverage");
is(0, $empty_genome->is_high_coverage, "Empty db is not high coverage");
+
+#
+# Test if there is data
+#
+
+is(1, $genome->is_empty, "Human core database has genome data");
+is(0, $empty_genome->is_empty, "Empty database has no genome data");
+
#
# Test polyploid genome support
#
--
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