Bio::DB::BioSQL ReferenceAdaptor
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Summary
Bio::DB::BioSQL::ReferenceAdaptor - DESCRIPTION of Object
Package variables
No package variables defined.
Included modules
Bio::Annotation::DBLink
Bio::Annotation::Reference
Bio::DB::BioSQL::BasePersistenceAdaptor
Bio::DB::PersistentObjectI
Inherit
Bio::DB::BioSQL::BasePersistenceAdaptor
Synopsis
Give standard usage here
Description
Adaptor for Reference objects inside bioperl db
Methods
newDescriptionCode
get_persistent_slotsDescriptionCode
get_persistent_slot_valuesDescriptionCode
get_foreign_key_objectsDescriptionCode
attach_foreign_key_objectsDescriptionCode
store_childrenDescriptionCode
remove_childrenDescriptionCode
instantiate_from_rowDescriptionCode
populate_from_rowDescriptionCode
get_unique_key_queryDescriptionCode
add_associationDescriptionCode
_dbxref_adaptorDescriptionCode
_dblink_fkDescriptionCode
_crc64DescriptionCode
Methods description
newcode    nextTop
 Title   : new
Usage :
Function: Instantiates the persistence adaptor.
Example :
Returns :
Args :
get_persistent_slotscodeprevnextTop
 Title   : get_persistent_slots
Usage :
Function: Get the slots of the object that map to attributes in its respective
entity in the datastore.
Slots should be methods callable without an argument. Example : Returns : an array of method names constituting the serializable slots Args : the object about to be inserted or updated
get_persistent_slot_valuescodeprevnextTop
 Title   : get_persistent_slot_values
Usage :
Function: Obtain the values for the slots returned by get_persistent_slots(),
in exactly that order.
The reason this method is here is that sometimes the actual slot values need to be post-processed to yield the value that gets actually stored in the database. E.g., slots holding arrays will need some kind of join function applied. Another example is if the method call needs additional arguments. Supposedly the adaptor for a specific interface knows exactly what to do here. Since there is also populate_from_row() the adaptor has full control over mapping values to a version that is actually stored. Example : Returns : A reference to an array of values for the persistent slots of this object. Individual values may be undef. Args : The object about to be serialized. A reference to an array of foreign key objects if not retrievable from the object itself.
get_foreign_key_objectscodeprevnextTop
 Title   : get_foreign_key_objects
Usage :
Function: Gets the objects referenced by this object, and which
therefore need to be referenced as foreign keys in the
datastore.
Bio::Annotation::Reference has a virtual dbxref (e.g., the MEDLINE link) as foreign key. Virtual means that in the object model there is no such reference, but there is in the BioSQL schema. Example : Returns : an array of Bio::DB::PersistentObjectI implementing objects Args : The object about to be inserted or updated, or undef if the call is for a SELECT query. In the latter case return class or interface names that are mapped to the foreign key tables. Optionally, additional named parameters. A common parameter will be -fkobjs, with a reference to an array of foreign key objects that are not retrievable from the persistent object itself.
attach_foreign_key_objectscodeprevnextTop
 Title   : attach_foreign_key_objects
Usage :
Function: Attaches foreign key objects to the given object as far as
necessary.
This method is called after find_by_XXX() queries, not for INSERTs or UPDATEs. Bio::Annotation::Reference has a virtual dbxref (e.g., the MEDLINE link) as foreign key. Virtual means that in the object model there is no such reference, but there is in the BioSQL schema. Example : Returns : TRUE on success, and FALSE otherwise. Args : The object to which to attach foreign key objects. A reference to an array of foreign key values, in the order of foreign keys returned by get_foreign_key_objects().
store_childrencodeprevnextTop
 Title   : store_children
Usage :
Function: Inserts or updates the child entities of the given object in
the datastore.
Example : Returns : TRUE on success, and FALSE otherwise Args : The Bio::DB::PersistentObjectI implementing object for which the child objects shall be made persistent. Optionally, additional named parameters. A common parameter will be -assoc_objs, with a reference to an array of objects to which this object should be associated in the database if those objects are not retrievable from the persistent object itself.
remove_childrencodeprevnextTop
 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().
instantiate_from_rowcodeprevnextTop
 Title   : instantiate_from_row
Usage :
Function: Instantiates the class this object is an adaptor for, and populates
it with values from columns of the row.
This implementation call populate_from_row() to do the real job. Example : Returns : An object, or undef, if the row contains no values Args : A reference to an array of column values. The first column is the primary key, the other columns are expected to be in the order returned by get_persistent_slots(). Optionally, the object factory to be used for instantiating the proper class. The adaptor must be able to instantiate a default class if this value is undef.
populate_from_rowcodeprevnextTop
 Title   : populate_from_row
Usage :
Function: Instantiates the class this object is an adaptor for, and populates
it with values from columns of the row.
Usually a derived class will instantiate the proper class and pass it on to populate_from_row(). This method MUST be overridden by a derived object. Example : Returns : An object, or undef, if the row contains no values Args : The object to be populated. A reference to an array of column values. The first column is the primary key, the other columns are expected to be in the order returned by get_persistent_slots().
get_unique_key_querycodeprevnextTop
 Title   : get_unique_key_query
Usage :
Function: Obtain the suitable unique key slots and values as
determined by the attribute values of the given object and
the additional foreign key objects, in case foreign keys
participate in a UK.
Example : Returns : One or more references to hash(es) where each hash represents one unique key, and the keys of each hash represent the names of the object's slots that are part of the particular unique key and their values are the values of those slots as suitable for the key. Args : The object with those attributes set that constitute the chosen unique key (note that the class of the object will be suitable for the adaptor). A reference to an array of foreign key objects if not retrievable from the object itself.
add_associationcodeprevnextTop
 Title   : add_assocation
Usage :
Function: Stores the association between given objects in the datastore.
We override this here to add start() and end() to the values hash. Everything else is left untouched and passed on to the inherited implementation. Example : Returns : TRUE on success and FALSE otherwise Args : Named parameters. At least the following must be recognized: -objs a reference to an array of objects to be associated with each other -values a reference to a hash the keys of which are abstract column names and the values are values of those columns. These columns are generally those other than the ones for foreign keys to the entities to be associated -obj_contexts optional, if given it denotes a reference to an array of context keys (strings), which allow the foreign key name to be determined through the association map rather than through foreign_key_name(). This is necessary if more than one object of the same type takes part in the association. The array must be in the same order as -objs, and have the same number of elements. Put "default" for objects for which there are no multiple contexts. Caveats: Make sure you *always* give the objects to be associated in the same order.
_dbxref_adaptorcodeprevnextTop
 Title   : _dbxref_adaptor
Usage : $obj->_dbxref_adaptor($newval)
Function: Get/set cached persistence adaptor for a bioperl DBLink object.
In OO speak, consider the access class of this method protected. I.e., call from descendants, but not from outside. Example : Returns : value of _dbxref_adaptor (a Bio::DB::PersistenceAdaptorI instance) Args : new value (a Bio::DB::PersistenceAdaptorI instance, optional)
_dblink_fkcodeprevnextTop
 Title   : _dblink_fk
Usage : $fk_dbl = $obj->_dblink_fk()
Function: Get the Bio::Annotation::DBLink object representing
the foreign key of references to their db_xref, if there
is a medline ID.
Example :
Returns : A persistent Bio::Annotation::DBLink object
Args : The Bio::Annotation::Reference object for which to emulate
the foreign key object
_crc64codeprevnextTop
 Title   : _crc64
Usage :
Function: Computes and returns the CRC64 checksum for a given
reference object.
The method uses the reference's authors, title, and location properties. Example : Returns : the CRC64 as a string Args : the Bio::Annotation::Reference object for which to compute the CRC
Methods code
newdescriptionprevnextTop
sub new {
   my ($class,@args) = @_;

   # we want to enable object caching
push(@args, "-cache_objects", 1) unless grep { /cache_objects/i; } @args; my $self = $class->SUPER::new(@args); return $self;
}
get_persistent_slotsdescriptionprevnextTop
sub get_persistent_slots {
    my ($self,@args) = @_;

    return ("authors","title","location","doc_id","start","end","rank");
}
get_persistent_slot_valuesdescriptionprevnextTop
sub get_persistent_slot_values {
    my ($self,$obj,$fkobjs) = @_;
    my @vals = ($obj->authors(),
		$obj->title(),
		$obj->location(),
		$self->_crc64($obj),
		$obj->start(),
		$obj->end(),
                $obj->can('rank') ? $obj->rank() : undef,
		);
    return\@ vals;
}
get_foreign_key_objectsdescriptionprevnextTop
sub get_foreign_key_objects {
    my $self = shift;
    my $obj = shift;
    my $fk;

    if($obj) {
	$fk = $self->_dblink_fk($obj);
    }
    $fk = "Bio::Annotation::DBLink" unless $fk;
    return $fk;
}
attach_foreign_key_objectsdescriptionprevnextTop
sub attach_foreign_key_objects {
    my ($self,$obj,$fks) = @_;
    my $ok = 1;
    
    if($fks && @$fks && $fks->[0]) {
	my $dbl = $self->_dbxref_adaptor->find_by_primary_key($fks->[0]);
	if($dbl) {
	    if(uc($dbl->database()) eq "PUBMED") {
		$obj->pubmed($dbl->primary_id());
	    } else {
		# we treat everything else as MEDLINE. Not very clean.
$obj->medline($dbl->primary_id()); } } else { $ok = 0; } } return $ok;
}
store_childrendescriptionprevnextTop
sub store_children {
    return 1;
}
remove_childrendescriptionprevnextTop
sub remove_children {
    return 1;
}
instantiate_from_rowdescriptionprevnextTop
sub instantiate_from_row {
    my ($self,$row,$fact) = @_;
    my $obj;

    if($row && @$row) {
	if($fact) {
	    $obj = $fact->create_object();
	} else {
	    $obj = Bio::Annotation::Reference->new();
	}
        # in order to store rank we need a persistent object - sooner or later
# it will be turned into one anyway
if (!$obj->isa("Bio::DB::PersistentObjectI")) { $obj = $self->create_persistent($obj); } # now populate
$self->populate_from_row($obj, $row); } return $obj;
}
populate_from_rowdescriptionprevnextTop
sub populate_from_row {
    my ($self,$obj,$row) = @_;

    if(! ref($obj)) {
	$self->throw("\"$obj\" is not an object. Probably internal error.");
    }
    if($row && @$row) {
	$obj->authors($row->[1]) if $row->[1];
	$obj->title($row->[2]) if $row->[2];
	$obj->location($row->[3]) if $row->[3];
	$obj->start($row->[5]) if $row->[5];
	$obj->end($row->[6]) if $row->[6];
        $obj->rank($row->[7]) if $row->[7] && $obj->can('rank');
	if($obj->isa("Bio::DB::PersistentObjectI")) {
	    $obj->primary_key($row->[0]);
	}
	return $obj;
    }
    return undef;
}
get_unique_key_querydescriptionprevnextTop
sub get_unique_key_query {
    my ($self,$obj,$fkobjs) = @_;
    my @ukqueries = ();

    # UK is either the dbxref foreign key, or the (computed) identifier
# for this object
if($obj->medline()) { my $dbl = Bio::Annotation::DBLink->new(-database => "MEDLINE", -primary_id => $obj->medline); $dbl = $self->_dbxref_adaptor->find_by_unique_key($dbl); if($dbl) { push(@ukqueries, { 'medline' => $dbl->primary_key(), }); } } if($obj->pubmed()) { my $dbl = Bio::Annotation::DBLink->new(-database => "PUBMED", -primary_id => $obj->pubmed); $dbl = $self->_dbxref_adaptor->find_by_unique_key($dbl); if($dbl) { push(@ukqueries, { 'pubmed' => $dbl->primary_key(), }); } } # note that according to the BioSQL v1.0 schema location is mandatory,
# so this clause should always evaluate to true, at least if the
# annotation comes from a legitimate source (such as Genbank, UniProt, etc)
if($obj->authors() || $obj->title() || $obj->location()) { push(@ukqueries, { 'doc_id' => $self->_crc64($obj), }); } return @ukqueries;
}
add_associationdescriptionprevnextTop
sub add_association {
    my ($self,@args) = @_;
    my ($i);

    # get arguments
my ($objs, $values) = $self->_rearrange([qw(OBJS VALUES)], @args); # have we been called in error? If so, be graceful and return an error.
return undef unless $objs && @$objs; # figure out which one of the objects is the reference
my ($refobj) = grep { ref($_) && $_->isa("Bio::Annotation::Reference"); } @$objs; if($refobj) { $values->{'start'} = $refobj->start(); $values->{'end'} = $refobj->end(); } else { $self->warn("unable to figure out the Bio::Annotation::Reference ". "object to associate with something, expect problems"); } # pass on to the inherited impl.
return $self->SUPER::add_association(@args);
}
_dbxref_adaptordescriptionprevnextTop
sub _dbxref_adaptor {
    my ($self,$adp) = @_;
    if( defined $adp) {
	$self->{'_dbxref_adaptor'} = $adp;
    }
    if(! exists($self->{'_dbxref_adaptor'})) {
	$self->{'_dbxref_adaptor'} =
	    $self->db()->get_object_adaptor("Bio::Annotation::DBLink");
    }
    return $self->{'_dbxref_adaptor'};
}
_dblink_fkdescriptionprevnextTop
sub _dblink_fk {
    my $self = shift;
    my $obj = shift;
    my ($db,$id,$dbl);

    if($obj->medline()) {
	$db = "MEDLINE"; $id = $obj->medline();
    } elsif($obj->pubmed()) {
	$db = "PUBMED"; $id = $obj->pubmed();
    }
    if($db) {
	$dbl = Bio::Annotation::DBLink->new(-database => $db,
					    -primary_id => $id);
	$dbl = $self->_dbxref_adaptor->create_persistent($dbl);
    }
    return $dbl;
}
_crc64descriptionprevnextTop
sub _crc64 {
    my $self = shift;
    my $obj = shift;

    my $str =
	(defined($obj->authors) ? $obj->authors : "<undef>") .
	(defined($obj->title) ? $obj->title : "<undef>") .
	(defined($obj->location) ? $obj->location : "<undef>");	
    
    return 'CRC-'.$self->crc64($str);
      
}

1;
}
General documentation
FEEDBACKTop
Mailing ListsTop
User feedback is an integral part of the evolution of this
and other Bioperl modules. Send your references and suggestions preferably
to one of the Bioperl mailing lists.
Your participation is much appreciated.
  bioperl-l@bio.perl.org
Support Top
 
Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
Reporting BugsTop
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution.
Bug reports can be submitted via email or the web:
  bioperl-bugs@bio.perl.org
http://bugzilla.open-bio.org/
AUTHOR - Elia Stupka, Hilmar LappTop
Email elia@ebi.ac.uk
Email hlapp at gmx.net
APPENDIXTop
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Overridden Inherited MethodsTop
Internal methodsTop
 These are mostly private or 'protected.' Methods which are in the
latter class have this explicitly stated in their
documentation. 'Protected' means you may call these from derived
classes, but not from outside.