skip undef values (do not even mention them) when performing store via insert...

skip undef values (do not even mention them) when performing store via insert (and let SQL layer initialize undefined fields)

modules/Bio/EnsEMBL/Hive/DBSQL/BaseAdaptor.pm

@@ -39,6 +39,8 @@ use strict;
 no strict 'refs';   # needed to allow AUTOLOAD create new methods
 use DBI 1.6;        # the 1.6 functionality is important for detecting autoincrement fields and other magic.
 
+use Bio::EnsEMBL::Hive::Utils ('stringify');
+
 
 sub default_table_name {
     die "Please define table_name either by setting it via table_name() method or by redefining default_table_name() in your adaptor class";
@@ -220,20 +222,19 @@ sub _table_info_loader {
     my $table_name  = $self->table_name();
 
     my %column_set  = ();
-    my %name2type   = ();
     my $autoinc_id  = '';
     my @primary_key = $dbh->primary_key(undef, undef, $table_name);
 
     my $sth = $dbh->column_info(undef, undef, $table_name, '%');
     $sth->execute();
     while (my $row = $sth->fetchrow_hashref()) {
-        my ($position, $column_name, $column_type, $is_ai) = @$row{'ORDINAL_POSITION','COLUMN_NAME', 'TYPE_NAME', 'mysql_is_auto_increment'};
+        my ( $column_name, $column_type ) = @$row{'COLUMN_NAME', 'TYPE_NAME'};
+
+        # warn "ColumnInfo [$table_name/$column_name] = $column_type\n";
 
-        $column_set{$column_name}  = 1;
-        $name2type{$column_name}   = $column_type;
+        $column_set{$column_name}  = $column_type;
 
-        if( $is_ai  # careful! This is only supported by DBD::mysql and will not work with other drivers
-         or ($column_name eq $table_name.'_id')
+        if( ($column_name eq $table_name.'_id')
          or ($table_name eq 'analysis_base' and $column_name eq 'analysis_id') ) {    # a special case (historical)
             $autoinc_id = $column_name;
         }
@@ -488,6 +489,7 @@ sub store {
 
     foreach my $object (@$objects) {
             my ($columns_being_stored, $column_key) = (ref($object) eq 'HASH') ? $self->keys_to_columns($object) : ($all_storable_columns, '*all*');
+            my ($columns_being_stored, $column_key) = $self->keys_to_columns($object);
             # warn "COLUMN_KEY='$column_key'\n";
 
             my $this_sth;
@@ -500,9 +502,9 @@ sub store {
                 $this_sth = $hashed_sth{$column_key} = $self->prepare( $sql ) or die "Could not prepare statement: $sql";
             }
 
-            # warn "STORED_COLUMNS: ".join(', ', map { "`$_`" } @$columns_being_stored)."\n";
+            # warn "STORED_COLUMNS: ".stringify($columns_being_stored)."\n";
             my $values_being_stored = $self->slicer( $object, $columns_being_stored );
-            # warn "STORED_VALUES: ".join(', ', map { "'$_'" } @$values_being_stored)."\n";
+            # warn "STORED_VALUES: ".stringify($values_being_stored)."\n";
 
             my $return_code = $this_sth->execute( @$values_being_stored )
                     # using $return_code in boolean context allows to skip the value '0E0' ('no rows affected') that Perl treats as zero but regards as true:

modules/Bio/EnsEMBL/Hive/DBSQL/NakedTableAdaptor.pm

@@ -43,9 +43,9 @@ use base ('Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor');
 
 
 sub slicer {    # take a slice of the hashref (if only we could inline in Perl!)
-    my ($self, $object, $fields) = @_;
+    my ($self, $hashref, $fields) = @_;
 
-    return [ @$object{@$fields} ];
+    return [ @$hashref{@$fields} ];
 }
 
 
@@ -64,9 +64,9 @@ sub mark_stored {
 
 
 sub keys_to_columns {
-    my ($self, $object) = @_;
+    my ($self, $hashref) = @_;
 
-    my $sorted_keys = [ sort keys %$object ];
+    my $sorted_keys = [ sort keys %$hashref ];
 
     return ( $sorted_keys, join(', ', @$sorted_keys) );
 }

modules/Bio/EnsEMBL/Hive/DBSQL/ObjectAdaptor.pm

@@ -83,5 +83,16 @@ sub mark_stored {
 }
 
 
+sub keys_to_columns {
+    my ($self, $object) = @_;
+
+    my $autoinc_id  = $self->autoinc_id();
+    my $sorted_keys = [ sort grep { ($_ ne $autoinc_id) and defined($object->$_()) } keys %{ $self->column_set() } ];
+
+    return ( $sorted_keys, join(', ', @$sorted_keys) );
+}
+
+
+
 1;