BioPerl-DB

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

           (basically, it needs to implement dbh(), sth($key, $sth),
	    dbcontext(), and get_persistent_slots()).
	   The object to be updated.
           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 update_object{
    my ($self,$adp,$obj,$fkobjs) = @_;
    
    # obtain the object's slots to be serialized
    my @slots = $adp->get_persistent_slots($obj);
    # get the UPDATE statement 
    # is it cached?
    my $cache_key = 'UPDATE '.ref($adp).' '.join(';',@slots);
    my $sth = $self->get_sth($adp,$obj,$fkobjs,$cache_key,'update_object');
    # 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

lib/Bio/DB/BioSQL/Oracle/AnnotationCollectionAdaptorDriver.pm  view on Meta::CPAN

           (basically, it needs to implement dbh(), sth($key, $sth),
	    dbcontext(), and get_persistent_slots()).
	   The object to be updated.
           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 update_object{
    my ($self,$adp,$obj,$fkobjs) = @_;
    
    return 1;
}


1;

lib/Bio/DB/BioSQL/Oracle/BiosequenceAdaptorDriver.pm  view on Meta::CPAN

           (basically, it needs to implement dbh(), sth($key, $sth),
	    dbcontext(), and get_persistent_slots()).
	   The object to be updated.
           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 update_object{
    my ($self,$adp,$obj,$fkobjs) = @_;

    # see whether there are any values defined at all
    my $slotvals = $adp->get_persistent_slot_values($obj, $fkobjs);
    my $isdef = 0;
    foreach (@$slotvals) { $isdef ||= $_; last if $isdef; }
    # in the majority of cases this actually will be an update indeed - so
    # let's just go ahead and try if there are any values to update
    my $rv = -1;
    if($isdef) {

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

           (basically, it needs to implement dbh(), sth($key, $sth),
	    dbcontext(), and get_persistent_slots()).
	   The object to be updated.
           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 update_object{
    my ($self,$adp,$obj,$fkobjs) = @_;

    $self->throw_not_implemented();

}

=head2 _build_select_list

 Title   : _build_select_list
 Usage   :

lib/Bio/DB/BioSQL/Pg/AnnotationCollectionAdaptorDriver.pm  view on Meta::CPAN

           (basically, it needs to implement dbh(), sth($key, $sth),
	    dbcontext(), and get_persistent_slots()).
	   The object to be updated.
           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 update_object{
    my ($self,$adp,$obj,$fkobjs) = @_;

    return 1;
}


1;

lib/Bio/DB/BioSQL/Pg/BiosequenceAdaptorDriver.pm  view on Meta::CPAN

           (basically, it needs to implement dbh(), sth($key, $sth),
	    dbcontext(), and get_persistent_slots()).
	   The object to be updated.
           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 update_object{
    my ($self,$adp,$obj,$fkobjs) = @_;
    
    my $cache_key = 'SELECT UK '.ref($self);
    my $sth = $adp->sth($cache_key);
    if(! $sth) {
	# create and prepare sql
	my $table = $self->table_name($adp);
	my $ukname = $self->foreign_key_name("Bio::PrimarySeqI");
	my $sql = "SELECT $ukname FROM $table WHERE $ukname = ?";
	$adp->debug("preparing SELECT statement: $sql\n");

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

           (basically, it needs to implement dbh(), sth($key, $sth),
	    dbcontext(), and get_persistent_slots()).
	   The object to be updated.
           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 update_object{
    my ($self,$adp,$obj,$fkobjs) = @_;

    $self->throw_not_implemented();

}

=head2 _build_select_list

 Title   : _build_select_list
 Usage   :

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

           (basically, it needs to implement dbh(), sth($key, $sth),
	    dbcontext(), and get_persistent_slots()).
	   The object to be updated.
           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 update_object{
    my ($self,$adp,$obj,$fkobjs) = @_;
    
    return 1;
}


1;

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

           (basically, it needs to implement dbh(), sth($key, $sth),
	    dbcontext(), and get_persistent_slots()).
	   The object to be updated.
           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 update_object{
    my ($self,$adp,$obj,$fkobjs) = @_;
    
    my $cache_key = 'SELECT UK '.$self;
    my $sth = $adp->sth($cache_key);
    if(! $sth) {
	# create and prepare sql
	my $table = $self->table_name($adp);
	my $ukname = $self->foreign_key_name("Bio::PrimarySeqI");
	my $sql = "SELECT $ukname FROM $table WHERE $ukname = ?";
	$adp->debug("preparing SELECT statement: $sql\n");

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

           (basically, it needs to implement dbh(), sth($key, $sth),
	    dbcontext(), and get_persistent_slots()).
	   The object to be updated.
           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 update_object{
    my ($self,$adp,$obj,$fkobjs) = @_;

    $self->throw_not_implemented();

}

=head2 _build_select_list

 Title   : _build_select_list
 Usage   :

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