RNAProduct + MicroRNA: increment hardcoded type_ids, AUTO_INCREMENT does not like zeros

modules/Bio/EnsEMBL/DBSQL/RNAProductAdaptor.pm

@@ -332,9 +332,9 @@ sub _fetch_direct_query {
 
     my $class_name;
     # FIXME: the usual thing about using type_id directly
-    if ($rnaproduct_type_id == 0) {
+    if ($rnaproduct_type_id == 1) {
       $class_name = 'Bio::EnsEMBL::RNAProduct';
-    } elsif ($rnaproduct_type_id == 1) {
+    } elsif ($rnaproduct_type_id == 2) {
       $class_name = 'Bio::EnsEMBL::MicroRNA';
     } else {
       throw("Unknown rnaproduct type");

modules/Bio/EnsEMBL/MicroRNA.pm

@@ -109,7 +109,7 @@ sub new { ## no critic (Subroutines::RequireArgUnpacking)
   my $self = $class->SUPER::new(@_);
 
   # FIXME: see the comment about same in RNAProduct::new()
-  my $type_id = 1;
+  my $type_id = 2;
 
   my ($arm) = rearrange(["ARM"], @_);
   $self->{'arm'} = $arm;

modules/Bio/EnsEMBL/RNAProduct.pm

@@ -105,7 +105,7 @@ sub new { ## no critic (Subroutines::RequireArgUnpacking)
   # RNA". Ideally we would look the corresponding ID up in rnaproduct_type,
   # then again that would make this dependent on the database connection...
   # Maybe we should just store a string code instead? Either way, FIXME.
-  my $type_id = 0;
+  my $type_id = 1;
 
   my ($seq_start, $seq_end, $stable_id, $version, $dbID, $adaptor, $seq,
       $created_date, $modified_date ) =
@@ -811,7 +811,7 @@ sub transcript {
 
 =head2 type_id
 
-  Example    : my $rp_type_id = $rnaproduct->type();
+  Example    : my $rp_type_id = $rnaproduct->type_id();
   Description: Getter for the RNAProduct type (e.g. miRNA, circRNA, ...).
                The type is expressed as a numerical ID and it is up to the
                user to look the details up in rnaproduct_type; it has been

modules/t/rnaProduct.t

@@ -85,7 +85,7 @@ ok(test_getter_setter($rp, 'created_date', time()), 'Test getter/setter created_
 ok(test_getter_setter($rp, 'modified_date', time()), 'Test getter/setter modified_date()');
 
 # FIXME: temporary, at least this way
-is($rp->type_id(), 0, 'type_id is zero (i.e. generic mature RNA)');
+is($rp->type_id(), 1, 'type_id is 1 (i.e. generic mature RNA)');
 
 subtest 'Test stable_id_version() functionality' =>  sub {
   ok(test_getter_setter($rp, 'stable_id_version', 3.14),
@@ -197,10 +197,10 @@ subtest 'fetch_all_by_type_id() functionality' => sub {
   # At the moment we have only got miRNA in the homo_sapiens test database
 
   # FIXME: compare this to the total number of RNAProducts?
-  $n_rps = scalar @{$rp_a->fetch_all_by_type_id(1)};
-  cmp_ok($n_rps, '>', 0, 'Got non-empty list of type_id==1 rnaproducts');
   $n_rps = scalar @{$rp_a->fetch_all_by_type_id(2)};
-  cmp_ok($n_rps, '==', 0, 'Got empty list of type_id==2 rnaproducts');
+  cmp_ok($n_rps, '>', 0, 'Got non-empty list of type_id==2 rnaproducts');
+  $n_rps = scalar @{$rp_a->fetch_all_by_type_id(3)};
+  cmp_ok($n_rps, '==', 0, 'Got empty list of type_id==3 rnaproducts');
 };
 
 $rp = undef;
@@ -212,7 +212,7 @@ $rp = $rp_a->fetch_by_stable_id('ENSM00000000001');
 ok($rp, 'Can fetch RNAProduct by stable ID');
 
 # FIXME: temporary, at least this way
-is($rp->type_id(), 1, 'type_id is 1 (i.e. miRNA)');
+is($rp->type_id(), 2, 'type_id is 2 (i.e. miRNA)');
 
 # FIXME: perform an in-depth inspection of one of the fetched RNAProducts,
 # to make sure new_fast() call all of these fetch methods use does what it

modules/t/transcript.t

@@ -1032,8 +1032,8 @@ for (my $i = 0; $i < scalar(@absolute_coords); $i++) {
 {
   $tr = $ta->fetch_by_stable_id('ENST00000278995');
   my $rps_all = $tr->get_all_RNAProducts();
-  my $rps_micro = $tr->get_all_RNAProducts(1);
-  my $rps_circ = $tr->get_all_RNAProducts(2);
+  my $rps_micro = $tr->get_all_RNAProducts(2);
+  my $rps_circ = $tr->get_all_RNAProducts(3);
 
   cmp_ok(scalar @{$rps_all}, '>', 0, 'Have RNA products');
   is_deeply($rps_all, $rps_micro, 'All RNA products are microRNAs');