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lib/Bio/DB/BioSQL/mysql/SpeciesAdaptorDriver.pm  view on Meta::CPAN

           placeholders as necessary for the given unique key.

           The statement is expected to return the primary key as the first and
           then as many columns as $adp->get_persistent_slots() returns, and in
           that order.
 Example :
 Returns : A DBI prepared statement handle with as many placeholders as 
           necessary for the given unique key
 Args    : The calling Bio::DB::BioSQL::BasePersistenceAdaptor derived object 
           (basically, it needs to implement dbh() and get_persistent_slots()).
           A reference to a hash with the names of the object''s slots in the
           unique key as keys and their values as values.
           A reference to an array of foreign key objects or slots 
           (class names if slot).


=cut

sub prepare_findbyuk_sth{
    my ($self,$adp,$ukval_h,$fkslots) = @_;

    # get the slot/attribute map
    my $table = $self->table_name($adp);
    my $node_table = $self->table_name("TaxonNode");
    my $pkname = $self->primary_key_name($node_table);
    my $fkname = $self->foreign_key_name("TaxonNode");
    my $slotmap = $self->slot_attribute_map($table);
    # SELECT columns
    my @attrs = $self->_build_select_list($adp,$fkslots);
    # WHERE clause constraints
    my @cattrs = ();
    foreach (keys %$ukval_h) {
	my $col;
	if(exists($slotmap->{$_})) {
	    $col = $slotmap->{$_};
	}
	push(@cattrs, $col || "NULL");
	$self->warn("slot $_ is in unique key, but can't be mapped to ".
		    "an entity column: you won't find anything")
	    unless $col;
    }
    # create the sql statement
    my $sql = "SELECT " . join(", ", @attrs) .
	" FROM $node_table, $table".
	" WHERE $node_table.$pkname = $table.$fkname AND ".
	join(" AND ", map { "$_ = ?"; } @cattrs);
    $adp->debug("preparing UK select statement: $sql\n");
    # prepare statement and return
    return $adp->dbh()->prepare($sql);
}

=head2 prepare_delete_sth

 Title   : prepare_delete_sth
 Usage   :
 Function: Creates a prepared statement with one placeholder variable suitable
           to delete one row from the respective table the given class maps to.

           We override this here in order to delete from the taxon
           node table, not the taxon name table. The node table will
           cascade to the name table.

 Example :
 Returns : A DBI statement handle for a prepared statement with one placeholder
 Args    : The calling adaptor (basically, it needs to implement dbh()).
           Optionally, additional arguments.


=cut

sub prepare_delete_sth{
    my ($self, $adp) = @_;

    # default is a simple DELETE statement
    #
    # we need the table name and the name of the primary key
    my $tbl = $self->table_name("TaxonNode");
    my $pkname = $self->primary_key_name($tbl);
    # straightforward SQL:
    my $sql = "DELETE FROM $tbl WHERE $pkname = ?";
    $adp->debug("preparing DELETE statement: $sql\n");
    my $sth = $adp->dbh()->prepare($sql);
    # done
    return $sth;
}

=head2 insert_object

 Title   : insert_object
 Usage   :
 Function:
 Example :
 Returns : The primary key of the newly inserted record.
 Args    : A Bio::DB::BioSQL::BasePersistenceAdaptor derived object
           (basically, it needs to implement dbh(), sth($key, $sth),
	    dbcontext(), and get_persistent_slots()).
	   The object to be inserted.
           A reference to an array of foreign key objects; if any of those
           foreign key values is NULL (some foreign keys may be nullable),
           then give the class name.


=cut

sub insert_object{
    my ($self,$adp,$obj,$fkobjs) = @_;
    
    # get the INSERT statements: we need one for the taxon node and one for
    # the taxon name table
    my $cache_key_t = 'INSERT taxon '.ref($obj);
    my $cache_key_tn = 'INSERT taxname '.ref($obj);
    my $sth_t = $adp->sth($cache_key_t);
    my $sth_tn = $adp->sth($cache_key_tn);
    my $sth_max = $adp->sth("SELECT MAX TAXON SETID");
    # we need the slot map regardless of whether we need to construct the
    # SQL or not, because we need to know which slots do not map to a column
    # (indicated by them being mapped to undef)
    my $table = $self->table_name($adp);
    my $node_table = $self->table_name("TaxonNode");
    my $fkname = $self->foreign_key_name("TaxonNode");
    my $slotmap = $self->slot_attribute_map($table);