Use hit_descritpion if external description not set (#651)

Co-authored-by: Tamara El Naboulsi <ten@codon-slurm-login-03.ebi.ac.uk>

lib/EnsEMBL/REST/Model/Overlap.pm

@@ -184,6 +184,11 @@ sub to_hash {
     if (lc($feature_type) eq 'gene') {
       $hash->{canonical_transcript} = $feature->canonical_transcript->stable_id.".".$feature->canonical_transcript->version;
     }
+    if (lc($feature_type) eq 'protein_feature') {
+      if (defined($hash->{description}) && !$hash->{description}) {
+        $hash->{description} = $feature->{$feature_type}->{hdescription} if defined($feature->{$feature_type}->{hdescription});
+      }
+    }
     push(@hashed, $hash);
   }
   return \@hashed;

t/info.t

@@ -177,7 +177,7 @@ is_json_GET(
   my $expected = [{ name => 'GO', description => undef, release => undef, display_name => 'GO' }];
   is_json_GET('/info/external_dbs/homo_sapiens?filter=GO', $expected, 'Checking GO filtering works');
   my $xref_external_dbs_json = json_GET('info/external_dbs/homo_sapiens?feature=xref', 'Get the xref external dbs hash');
-  is(scalar(@{$xref_external_dbs_json}), 38, 'Ensuring we have the right number of xref external_dbs available');
+  is(scalar(@{$xref_external_dbs_json}), 39, 'Ensuring we have the right number of xref external_dbs available');
 
   action_bad_regex('/info/external_dbs/wibble', qr/Could not fetch adaptor for species .+/, 'Bogus species means error message');
 }

t/overlap.t

@@ -543,6 +543,46 @@ $base = '/overlap/translation';
   eq_or_diff($json->[0], $expected, 'Checking that the overlap is at the expected location');
 }
 
+# Check that the correct description is returned
+{
+  my $id = 'ENSP00000371073';
+  cmp_deeply(json_GET("$base/$id?type=smart", 'Ensembl Smart domains'), [{
+    cigar_string => '',
+    type => 'Smart',
+    translation_id => 725227,
+    start => 33,
+    description => 'plcx_3',
+    interpro => '',
+    end => 202,
+    align_type => undef,
+    Parent => 'ENST00000381657',
+    feature_type => 'protein_feature',
+    hit_start => 1,
+    hseqname => 'SM00148',
+    seq_region_name => 'ENSP00000371073',
+    id => 'SM00148',
+    hit_end => 182
+  }], 'Protein feature description displayed for \'Smart\' type');
+
+  cmp_deeply(json_GET("$base/$id?type=pfam", 'Ensembl Pfam domains'), [{
+    feature_type => 'protein_feature',
+    hit_start => 24,
+    align_type => undef,
+    translation_id => 725227,
+    cigar_string => '',
+    start => 84,
+    seq_region_name => 'ENSP00000371073',
+    Parent => 'ENST00000381657',
+    hit_end => 120,
+    interpro => 'IPR000001',
+    hseqname => 'PF00388',
+    id => 'PF00388',
+    type => 'Pfam',
+    description => 'Kringle',
+    end => 183
+  }], 'Interpro description displayed for \'Pfam\' type');
+}
+
 # Test retrieving variation features where no variation db exists
 {
   my $base = '/overlap/region/meleagris_gallopavo';
@@ -567,5 +607,4 @@ $base = '/overlap/translation';
   is(scalar(@{$json}), 1, '1 somatic structural variation feature overlaps input region');
 }
 
-
 done_testing();

t/test-genome-DBs/homo_sapiens/core/interpro.txt

+IPR000001	PF00388

t/test-genome-DBs/homo_sapiens/core/protein_feature.txt

@@ -71,9 +71,9 @@
 3914981	725225	35	155	0	0	PS50007	8291	10.501	0	0	\N	\N	\N	\N
 3914982	725226	18	88	0	0	SSF51695	8288	0	0.000000000048	0	\N	\N	\N	\N
 3914983	725226	35	76	0	0	PS50007	8291	8.507	0	0	\N	\N	\N	\N
-3914984	725227	84	183	24	120	PF00388	8287	33.3	0.0000000000019	0	\N	\N	\N	\N
+3914984	725227	84	183	24	120	PF00388	8287	33.3	0.0000000000019	0	\N	PI-PLC-X	\N	\N
 3914985	725227	18	319	0	0	SSF51695	8288	0	9e-67	0	\N	\N	\N	\N
-3914986	725227	33	202	1	182	SM00148	8289	-32.9	0.0011	0	\N	\N	\N	\N
+3914986	725227	33	202	1	182	SM00148	8289	-32.9	0.0011	0	\N	plcx_3	\N	\N
 3914987	725227	35	179	0	0	PS50007	8291	12.652	0	0	\N	\N	\N	\N
 3914988	725228	18	60	0	0	SSF51695	8288	0	0.0000000018	0	\N	\N	\N	\N
 3914989	725229	18	64	0	0	SSF51695	8288	0	0.0000000005	0	\N	\N	\N	\N

t/test-genome-DBs/homo_sapiens/core/xref.txt

@@ -756,3 +756,4 @@
 3656321	4610	OTTHUMT00000460262	OTTHUMT00000460262	1	\N	NONE	
 3656322	12410	RP11-66N11.8-001	RP11-66N11.8-001	0		DIRECT	
 3656323	20046	ENSG00000073614	ENSG00000073614	0		DIRECT	
+3656324	1200	IPR000001	Kringle	0	Kringle	DIRECT	\N