BioPerl-DB

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

    # return type
    return $foundanything ?
	Bio::DB::Query::PrebuiltResult->new(-objs => [$ac]) :
	Bio::DB::Query::PrebuiltResult->new(-objs => []);
}

=head2 remove_children

 Title   : remove_children
 Usage   :
 Function: This method is to cascade deletes in maintained objects.

           We need to undefine the primary keys of all contained
           children objects here.

 Example :
 Returns : TRUE on success and FALSE otherwise
 Args    : The persistent object that was just removed from the database.
           Additional (named) parameter, as passed to remove().

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

    # get the annotation type map
    my $annotmap = $self->_supported_annotation_map();
    # check annotation for each key
    foreach my $annkey ($ac->get_all_annotation_keys()) {
	foreach my $ann ($ac->get_Annotations($annkey)) {
	    if($ann->isa("Bio::DB::PersistentObjectI")) {
		# undef the PK if this is a child relationship by FK
		my $key = $self->_annotation_map_key($annotmap,$ann);
		if($annotmap->{$key}->{"link"} eq "child") {
		    $ann->primary_key(undef);
		    # cascade through in case the object needs it
		    $ann->adaptor->remove_children($ann);
		}
	    }
	}
    }
    # done
    return 1;
}

=head1 Internal Methods

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

	}
    }
    my $ifnull = $adp->dbcontext->dbi->ifnull_sqlfunc();
    my $sql = "UPDATE $table SET " .
	join(", ", map {"$_ = $ifnull\(?,$_\)";} @attrs) .
	" WHERE " . $self->primary_key_name($table) . " = ?";
    $adp->debug("preparing UPDATE statement: $sql\n");
    return $self->prepare($adp->dbh(),$sql);
}

=head2 cascade_delete

 Title   : cascade_delete
 Usage   :
 Function: Removes all persistent objects dependent from the given persistent
           object from the database (foreign key integrity).

           This implementation assumes that the underlying schema and RDBMS
           support cascading deletes, and hence does nothing other than 
           returning TRUE.
 Example :
 Returns : TRUE on success, and FALSE otherwise
 Args    : The DBContextI implementing object for the database.
           The object for which the dependent rows shall be deleted. 
           Optionally, additional (named) arguments.


=cut

sub cascade_delete{
    # our default assumption is that the RDBMS does support cascading deletes
    return 1;
}

=head2 insert_object

 Title   : insert_object
 Usage   :
 Function:
 Example :

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

    my $foundobj;
    if($self->caching_mode() &&
       ($foundobj = $self->find_by_unique_key($obj, @args))) {
	$obj->primary_key($foundobj->primary_key);
	# Should we return right here instead of storing children? Not sure.
	#
	# My take is that we shouldn't store the children for found objects,
	# because it essentially would amount to updating dependent
	# information, which is inconsistent with the fact that we don't
	# update the object itself. So, leave it to the caller to physically
	# trigger an update (which will cascade through to the children)
	# instead of doing possibly unwanted magic here.
	# 
	$skip_children = 1 unless defined($skip_children);
    } else {
	# either caching disabled or not found in cache
	#
	# insert and obtain primary key
	my $pk = $self->dbd()->insert_object($self, $obj, \@fkobjs);
	# if no primary key, it may be due to a UK violation (provided that
	# caching is disabled)

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

    if(! $sth) {
	# need to create one
	$sth = $self->dbd()->prepare_delete_sth($self, @args);
	# and cache
	$self->sth($cache_key, $sth);
    }
    # execute
    my ($rv, $rv2);
    $self->debug("DELETING ".ref($obj->obj())." object (pk=$pk)\n");
    $rv = $sth->execute($pk);
    # we may need to cascade in software -- ugly
    $rv2 = $self->dbd()->cascade_delete($self->dbcontext(), $obj) if $rv;
    # the caller should commit if necessary
    #
    # take care of the children (do this before undefining the primary key
    # as something might have children that need this to locate them)
    $rv = $self->remove_children($obj,@args) ? $rv : 0;
    # undefine the objects primary key - it doesn't exist in the datastore any
    # longer
    $obj->primary_key(undef);
    # done
    return $rv;

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

=cut

sub attach_children{
    return 1;
}

=head2 remove_children

 Title   : remove_children
 Usage   :
 Function: This method is to cascade deletes in maintained objects.

           Child records in the database will usually be cascaded by
           the RDBMS. In order to cascade removals to persistent child
           objects, you must override this method. Usually you will
           need to undefine the primary key of child objects, and
           possibly remove them from caches if they are cached.

           Because failure to do so may result in serious and often
           non-obvious bugs, there is no default provided here. You
           *must* override this method in a derived adaptor as
           evidence that you know what you are doing, even if all you
           do is just return TRUE.

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

	$uk_h->{'namespace'} = $obj->namespace();
    } 
    
    return $uk_h;
}

=head2 remove_children

 Title   : remove_children
 Usage   :
 Function: This method is to cascade deletes in maintained objects.

           We just return TRUE here.

 Example :
 Returns : TRUE on success and FALSE otherwise
 Args    : The persistent object that was just removed from the database.
           Additional (named) parameter, as passed to remove().


=cut

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

=cut

sub attach_foreign_key_objects{
    return 1;
}

=head2 remove_children

 Title   : remove_children
 Usage   :
 Function: This method is to cascade deletes in maintained objects.

           We just return TRUE here.

 Example :
 Returns : TRUE on success and FALSE otherwise
 Args    : The persistent object that was just removed from the database.
           Additional (named) parameter, as passed to remove().


=cut

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

				       -contexts =>["subject","object",undef]);
    }
    # done
    return $ok;
}

=head2 remove_children

 Title   : remove_children
 Usage   :
 Function: This method is to cascade deletes in maintained objects.

           We need to undefine the primary keys of all contained
           annotation objects here.

 Example :
 Returns : TRUE on success and FALSE otherwise
 Args    : The persistent object that was just removed from the database.
           Additional (named) parameter, as passed to remove().

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

=cut

sub attach_foreign_key_objects{
    return 1;
}

=head2 remove_children

 Title   : remove_children
 Usage   :
 Function: This method is to cascade deletes in maintained objects.

           We just return TRUE here.

 Example :
 Returns : TRUE on success and FALSE otherwise
 Args    : The persistent object that was just removed from the database.
           Additional (named) parameter, as passed to remove().


=cut

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

=cut

sub store_children{
    return 1;
}

=head2 remove_children

 Title   : remove_children
 Usage   :
 Function: This method is to cascade deletes in maintained objects.

           We just return TRUE here.

 Example :
 Returns : TRUE on success and FALSE otherwise
 Args    : The persistent object that was just removed from the database.
           Additional (named) parameter, as passed to remove().


=cut

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

sub store_children{
    my ($self,$obj) = @_;

    return 1;
}

=head2 remove_children

 Title   : remove_children
 Usage   :
 Function: This method is to cascade deletes in maintained objects.

           We just return TRUE here.

 Example :
 Returns : TRUE on success and FALSE otherwise
 Args    : The persistent object that was just removed from the database.
           Additional (named) parameter, as passed to remove().


=cut

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

    my @vals = ($obj->name(),
		$obj->definition()
		);
    return \@vals;
}

=head2 remove_children

 Title   : remove_children
 Usage   :
 Function: This method is to cascade deletes in maintained objects.

           We just return TRUE here.

 Example :
 Returns : TRUE on success and FALSE otherwise
 Args    : The persistent object that was just removed from the database.
           Additional (named) parameter, as passed to remove().


=cut

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

=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{

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

=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{

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

    my ($self,$obj) = @_;

    # delegate to Biosequence adaptor
    return $self->_bioseq_adaptor()->store($obj);
}

=head2 remove_children

 Title   : remove_children
 Usage   :
 Function: This method is to cascade deletes in maintained objects.

           We just return TRUE here.

 Example :
 Returns : TRUE on success and FALSE otherwise
 Args    : The persistent object that was just removed from the database.
           Additional (named) parameter, as passed to remove().


=cut

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

=cut

sub store_children{
    return 1;
}

=head2 remove_children

 Title   : remove_children
 Usage   :
 Function: This method is to cascade deletes in maintained objects.

           We just return TRUE here, because the dbxref child is only
           virtual.

 Example :
 Returns : TRUE on success and FALSE otherwise
 Args    : The persistent object that was just removed from the database.
           Additional (named) parameter, as passed to remove().

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

	    $obj->ontology($ont) if $ont;
	}
    }
    return $ok;
}

=head2 remove_children

 Title   : remove_children
 Usage   :
 Function: This method is to cascade deletes in maintained objects.

           We just return TRUE here.

 Example :
 Returns : TRUE on success and FALSE otherwise
 Args    : The persistent object that was just removed from the database.
           Additional (named) parameter, as passed to remove().


=cut

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

    if($obj && $rows && @$rows && $obj->isa("Bio::Seq::RichSeqI")) {
	$obj->division($rows->[6]) if $rows->[6];
    }
    return $obj;
}

=head2 remove_children

 Title   : remove_children
 Usage   :
 Function: This method is to cascade deletes in maintained objects.

           We need to undefine the primary keys of all contained
           feature objects here.

 Example :
 Returns : TRUE on success and FALSE otherwise
 Args    : The persistent object that was just removed from the database.
           Additional (named) parameter, as passed to remove().


=cut

sub remove_children{
    my $self = shift;
    my $obj = shift;

    # features
    foreach my $feat ($obj->top_SeqFeatures()) {
	if($feat->isa("Bio::DB::PersistentObjectI")) {
	    $feat->primary_key(undef);
	    # cascade to feature's children
	    $self->_feat_adaptor->remove_children($feat);
	}
    }
    # annotation collection
    my $ac = $obj->annotation();
    if($ac->isa("Bio::DB::PersistentObjectI")) {
	$ac->primary_key(undef);
	$ac->adaptor()->remove_children($ac);
    }
    # done

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

    # annotation adaptor added everything to the feature transparently
    $qres->next_object(); # remove it from the stack, just to be sure
    # done
    return $ok;
}

=head2 remove_children

 Title   : remove_children
 Usage   :
 Function: This method is to cascade deletes in maintained objects.

           We need to undefine the primary keys of location objects
           here.

 Example :
 Returns : TRUE on success and FALSE otherwise
 Args    : The persistent object that was just removed from the database.
           Additional (named) parameter, as passed to remove().

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

=cut

sub attach_children{
    return 1;
}

=head2 remove_children

 Title   : remove_children
 Usage   :
 Function: This method is to cascade deletes in maintained objects.

           We just return TRUE here.

 Example :
 Returns : TRUE on success and FALSE otherwise
 Args    : The persistent object that was just removed from the database.
           Additional (named) parameter, as passed to remove().


=cut

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

	$uk_h->{'name_class'} = "scientific name";
    }
    
    return $uk_h;
}

=head2 remove_children

 Title   : remove_children
 Usage   :
 Function: This method is to cascade deletes in maintained objects.

           We just return TRUE here.

 Example :
 Returns : TRUE on success and FALSE otherwise
 Args    : The persistent object that was just removed from the database.
           Additional (named) parameter, as passed to remove().


=cut

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

    # in bioperl - although they could be)
    $ok = $self->get_synonyms($obj) && $ok;
    # done
    return $ok;
}

=head2 remove_children

 Title   : remove_children
 Usage   :
 Function: This method is to cascade deletes in maintained objects.


 Example :
 Returns : TRUE on success and FALSE otherwise
 Args    : The persistent object that was just removed from the database.
           Additional (named) parameter, as passed to remove().


=cut

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

=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{

lib/Bio/DB/DBD.pm  view on Meta::CPAN

=cut

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

    $self->throw_not_implemented();
}

=head2 cascade_delete

 Title   : cascade_delete
 Usage   :
 Function: Removes all persistent objects dependent from the given persistent
           object from the database (foreign key integrity).

           The method may throw an exception, or the database calls
           involved may throw an exception.

           If the RDBMS supports cascading deletes, and the schema definition
           enabled FK constraints with cascading deletes, then the
           implementation won''t need to do anything.
 Example :
 Returns : TRUE on success, and FALSE otherwise
 Args    : The DBContextI implementing object for the database.
           The object for which the dependent rows shall be deleted. 
           Optionally, additional (named) arguments.


=cut

sub cascade_delete{
    my ($self,@args) = @_;

    $self->throw_not_implemented();
}

1;