[ENSCORESW-745]. Homology endpoints no longer throws an error when querying the same species.

Before we had some bizarre behaviour by trying to query for a MLSS with the same species mentioned twice. That
no longer happens. We can query for self homologies if needed. Also we do not try to find bad MLSS sets.

lib/EnsEMBL/REST/Controller/Compara.pm

@@ -165,27 +165,72 @@ sub _method_link_species_sets {
   else {
     @types = qw/ENSEMBL_ORTHOLOGUES ENSEMBL_PARALOGUES/;
   }
+
+  my %unique_genome_dbs;
+  my @mlss_queries;
+  my $registry = $c->model('Registry');
+  my $source_gdb = $member->genome_db();
+  my $source_gdb_id = $source_gdb->dbID();
   
   #If someone has requested species then limit by MLSS
   my @target_species = $c->request->param('target_species');
-  my $source_name = $member->genome_db()->name();  
   foreach my $target (@target_species) {
-    foreach my $ml_type (@types) {
-      my $r = $mlssa->fetch_by_method_link_type_registry_aliases($ml_type, [$source_name, $target]);
-      push(@mlss, $r);
+    my $species_name = $registry->get_alias($target);
+    if(! $species_name) {
+      $c->go('ReturnError', 'custom', "Nothing is known to this server about the species name '${target}'");
+    }
+    my $gdb;
+    try {
+      $gdb = $gdba->fetch_by_name_assembly($species_name);
+    } catch {
+      my $meta_c = $registry->get_adaptor($species_name, 'core', 'MetaContainer');
+      $gdb = $gdba->fetch_by_name_assembly($meta_c->get_production_name());
+    };
+    if($gdb) {
+      next if exists $unique_genome_dbs{$gdb->dbID()};
+      if($gdb->dbID() == $source_gdb_id) {
+        push(@mlss_queries, [$source_gdb]);
+      }
+      else {
+        push(@mlss_queries, [$source_gdb, $gdb]);
+      }
+      $unique_genome_dbs{$gdb->dbID()} = 1;
+    }
+    else {
+      $c->go('ReturnError', 'custom', "Cannot convert '${target}' into a valid GenomeDB object. Please try again with a different value");
     }
   }
   
   #Could be taxon identifiers though
   my @target_taxons = $c->request->param('target_taxon');
-  my $source_gdb = $member->genome_db();
   foreach my $taxon (@target_taxons) {
     my $gdb = $gdba->fetch_by_taxon_id($taxon);
-    foreach my $ml_type (@types) {
-      my $gdbs = [$source_gdb, $gdb];
+    if($gdb) {
+      next if exists $unique_genome_dbs{$gdb->dbID()};
+      if($gdb->dbID() == $source_gdb_id) {
+        push(@mlss_queries, [$source_gdb]);
+      }
+      else {
+        push(@mlss_queries, [$source_gdb, $gdb]);
+      }
+      $unique_genome_dbs{$gdb->dbID()} = 1;
+    }
+    else {
+      $c->go('ReturnError', 'custom', "Cannot convert taxon ID '${taxon}' into a valid GenomeDB object. Please try again with a different value");
+    }
+  }
+
+  # Now get the MLSSs
+  my $log = $c->log();
+  foreach my $ml_type (@types) {
+    foreach my $gdbs (@mlss_queries) {
+      my $genome_names = join(q{, }, map({$_->name()} @{$gdbs}));
+      if($log->is_debug()) {
+        $log->debug("Fetching MLSS for ${ml_type} and [${genome_names}]");
+      }
       my $r = $mlssa->fetch_by_method_link_type_GenomeDBs($ml_type, $gdbs);
       if(! $r) {
-        $c->log->info('Cannot get a MLSS for ', $ml_type, ' and [', map({$_->name()} @{$gdbs}), ']');
+        $log->debug("Cannot get a MLSS for ${ml_type} and [${genome_names}]");
         next;
       }
       push(@mlss, $r);

lib/EnsEMBL/REST/Model/Registry.pm

@@ -390,6 +390,15 @@ sub disconnect_DBAdaptors {
   return;
 }
 
+sub get_alias {
+  my ($self, $alias) = @_;
+  my $reg = $self->_registry();
+  if($reg->alias_exists($alias)) {
+    return $reg->get_alias($alias);
+  }
+  return;
+}
+
 __PACKAGE__->meta->make_immutable;
 
 1;