some fixes for multi-version support

modules/Bio/EnsEMBL/DBSQL/ExonAdaptor.pm

@@ -632,7 +632,7 @@ sub _objs_from_sth {
 	'-modified_date' =>  $modified_date || undef,
         '-phase'         =>  $phase,
         '-end_phase'     =>  $end_phase,
-        'is_current'     =>  $is_current
+        '-is_current'    =>  $is_current
     );
 
   }

modules/Bio/EnsEMBL/Exon.pm

@@ -75,17 +75,17 @@ use vars qw(@ISA);
                 the slice it is sitting on.  Coordinates start at 1 and are
                 inclusive.
   Arg [-STRAND]: The orientation of this feature.  Valid values are 1,-1,0.
-  Arg [-SEQNAME] : A seqname to be used instead of the default name of the
-                of the slice.  Useful for features that do not have an
+  Arg [-SEQNAME] : (optional) A seqname to be used instead of the default name
+                of the of the slice.  Useful for features that do not have an
                 attached slice such as protein features.
   Arg [-dbID]   : (optional) internal database id
   Arg [-ADAPTOR]: (optional) Bio::EnsEMBL::DBSQL::BaseAdaptor
-  Arg [-PHASE]    :(optional) the phase. 
-  Arg [-END_PHASE]:(optional) the end phase
-  Arg [-STABLE_ID]:(optional) the stable id of the exon
-  Arg [-VERSION]  :(optional) the version
-  Arg [-CREATED_DATE] :(optional) the created date
-  Arg [-MODIFIED_DATE]:(optional) the last midifeid date
+  Arg [-PHASE]    : the phase. 
+  Arg [-END_PHASE]: the end phase
+  Arg [-STABLE_ID]: (optional) the stable id of the exon
+  Arg [-VERSION]  : (optional) the version
+  Arg [-CREATED_DATE] : (optional) the created date
+  Arg [-MODIFIED_DATE]: (optional) the last midifeid date
 
   Example    : none
   Description: create an Exon object
@@ -114,7 +114,10 @@ sub new {
   $self->{'version'} = $version;
   $self->{'created_date'} = $created_date;
   $self->{'modified_date'} = $modified_date;
-  $self->{'is_current'} if (defined($is_current));
+
+  # default is_current
+  $is_current = 1 unless (defined($is_current));
+  $self->{'is_current'} = $is_current;
 
   return $self;
 }

modules/Bio/EnsEMBL/Gene.pm

@@ -139,7 +139,10 @@ sub new {
                                 # kept to ensure routine is backwards compatible.
   $self->status( $status);      # add new naming
   $self->source( $source );
-  $self->is_current($is_current) if (defined($is_current));
+
+  # default to is_current
+  $is_current = 1 unless (defined($is_current));
+  $self->{'is_current'} = $is_current;
 
   return $self;
 }

modules/Bio/EnsEMBL/Transcript.pm

@@ -151,7 +151,10 @@ sub new {
   $self->status( $confidence );  # old style name
   $self->status( $status );      # new style name
   $self->biotype( $biotype );
-  $self->is_current($is_current) if (defined($is_current));
+
+  # default is_current
+  $is_current = 1 unless (defined($is_current));
+  $self->{'is_current'} = $is_current;
 
   return $self;
 }

modules/t/exon.t

@@ -2,7 +2,7 @@ use strict;
 
 BEGIN { $| = 1;
 	use Test ;
-	plan tests => 31;
+	plan tests => 35;
 }
 
 my $loaded = 0;
@@ -210,8 +210,9 @@ ok(count_rows($db, 'supporting_feature') == $supfeat_count - $supfeat_minus);
 
 $multi->restore();
 
-
+#
 # tests for multiple versions of transcripts in a database
+#
 
 $exon = $exonad->fetch_by_stable_id('ENSE00001109603');
 debug("fetch_by_stable_id");
@@ -221,4 +222,45 @@ my @exons = @{ $exonad->fetch_all_versions_by_stable_id('ENSE00001109603') };
 debug("fetch_all_versions_by_stable_id");
 ok( scalar(@exons) == 2 );
 
+# store/update tests
+
+$multi->hide( "core", "exon", "supporting_feature", 
+	      "protein_align_feature", "dna_align_feature");
+
+my $e1 = Bio::EnsEMBL::Exon->new(
+  -start => 10,
+  -end => 1000,
+  -strand => 1,
+  -slice => $slice,
+  -phase => 0,
+  -end_phase => 0,
+  -stable_id => 'ENSE0001',
+  -version => 1
+);
+
+my $e2 = Bio::EnsEMBL::Exon->new(
+  -start => 10,
+  -end => 1000,
+  -strand => 1,
+  -slice => $slice,
+  -phase => 0,
+  -end_phase => 0,
+  -stable_id => 'ENSE0001',
+  -version => 2,
+  -is_current => 0
+);
+
+$exonad->store($e1);
+$exonad->store($e2);
+
+$exon = $exonad->fetch_by_stable_id('ENSE0001');
+ok( $exon->is_current == 1);
+
+@exons = @{ $exonad->fetch_all_versions_by_stable_id('ENSE0001') };
+foreach my $e (@exons) {
+  next unless ($e->version == 2);
+  ok($e->is_current == 0);
+}
+
+$multi->restore();
 

modules/t/gene.t

@@ -3,7 +3,7 @@ use warnings;
 
 BEGIN { $| = 1;
 	use Test;
-	plan tests => 76;
+	plan tests => 81;
 }
 
 use Bio::EnsEMBL::Test::MultiTestDB;
@@ -643,7 +643,9 @@ $gene = $ga->fetch_by_dbID(18271);
 my @factors = @{$gene->fetch_coded_for_regulatory_factors()};
 ok($factors[0]->dbID() == 5);
 
+#
 # tests for multiple versions of genes in a database
+#
 
 $gene = $ga->fetch_by_stable_id('ENSG00000355555');
 debug("fetch_by_stable_id");
@@ -681,3 +683,45 @@ $gene = $ga->fetch_by_dbID(18276);
 debug("fetch_by_dbID, non current");
 ok( $gene->is_current == 0 );
 
+# store/update
+
+$gene = $ga->fetch_by_stable_id('ENSG00000355555');
+foreach my $t (@{ $gene->get_all_Transcripts }) {
+  $t->get_all_Exons;
+}
+
+$multi->hide( "core", "gene", "transcript", "exon", 'xref', 'object_xref',
+              "exon_transcript", "translation", "gene_stable_id" );
+
+$gene->version(3);
+$gene->dbID(undef);
+$gene->adaptor(undef);
+$ga->store($gene);
+
+$gene->version(4);
+$gene->is_current(0);
+$gene->dbID(undef);
+$gene->adaptor(undef);
+$ga->store($gene);
+
+$gene = $ga->fetch_by_stable_id('ENSG00000355555');
+ok($gene->is_current == 1);
+
+@genes = @{ $ga->fetch_all_versions_by_stable_id('ENSG00000355555') };
+foreach my $g (@genes) {
+  next unless ($g->version == 4);
+  ok($g->is_current == 0);
+}
+
+$gene->is_current(0);
+$ga->update($gene);
+my $g1 = $ga->fetch_by_stable_id('ENSG00000355555');
+ok(!$g1);
+
+$gene->is_current(1);
+$ga->update($gene);
+$gene = $ga->fetch_by_stable_id('ENSG00000355555');
+ok($gene->is_current == 1);
+
+$multi->restore;
+

modules/t/transcript.t

@@ -4,7 +4,7 @@ use vars qw( $verbose );
 
 BEGIN { $| = 1;
 	use Test;
-	plan tests => 140;
+	plan tests => 152;
 }
 
 use Bio::EnsEMBL::Test::MultiTestDB;
@@ -117,7 +117,7 @@ ok ( $tr->display_xref->dbID() == 97759 );
 ok( test_getter_setter( $tr, "display_xref", 42 ));
 
 ok( test_getter_setter( $tr, "dbID", 100000 ));
-ok( test_getter_setter( $tr, "type", "NOVEL" ));
+ok( test_getter_setter( $tr, "biotype", "NOVEL" ));
 ok( test_getter_setter( $tr, "created_date", time() ));
 ok( test_getter_setter( $tr, "modified_date", time() ));
 
@@ -501,7 +501,9 @@ ok(count_rows($db, 'transcript_attrib') == 2);
 
 $multi->restore('core');
 
+#
 # tests for multiple versions of transcripts in a database
+#
 
 $tr = $ta->fetch_by_stable_id('ENST00000355555');
 debug("fetch_by_stable_id");
@@ -536,6 +538,52 @@ $tr = $ta->fetch_by_display_label('MX_HUMAN');
 debug("fetch_by_display_label");
 ok( $tr->dbID == 21740 );
 
+# store/update
+
+$tr = $ta->fetch_by_stable_id('ENST00000355555');
+$g = $db->get_GeneAdaptor->fetch_by_transcript_id($tr->dbID);
+$tr->get_all_Exons;
+
+$multi->hide( "core", "gene", "transcript", "exon", 'xref', 'object_xref',
+              "exon_transcript", "translation", "transcript_stable_id" );
+
+$tr->version(3);
+$tr->dbID(undef);
+$tr->adaptor(undef);
+$ta->store($tr, $g->dbID);
+
+$tr->version(4);
+$tr->is_current(0);
+$tr->dbID(undef);
+$tr->adaptor(undef);
+$ta->store($tr, $g->dbID);
+
+$tr = $ta->fetch_by_stable_id('ENST00000355555');
+ok($tr->is_current == 1);
+
+@transcripts = @{ $ta->fetch_all_versions_by_stable_id('ENST00000355555') };
+foreach my $t (@transcripts) {
+  next unless ($t->version == 4);
+  ok($t->is_current == 0);
+}
+
+$tr->is_current(0);
+$ta->update($tr);
+my $t1 = $ta->fetch_by_stable_id('ENST00000355555');
+ok(!$t1);
+
+$tr->is_current(1);
+$ta->update($tr);
+$tr = $ta->fetch_by_stable_id('ENST00000355555');
+ok($tr->is_current == 1);
+
+$multi->restore;
+
+
+#
+# end main
+#
+
 
 sub test_trans_mapper_edits {
   $tr->edits_enabled(1);