[MOBY-guts] biomoby commit

[Dirk Haase]

d.haase
Tue Jan 30 09:57:47 EST 2007
Update of /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby
In directory dev.open-bio.org:/tmp/cvs-serv2011

Modified Files:
	queryapi.pm 
Log Message:
Added interfaces for new methods 'get_all_relationships' and 'get_details_for_id_list'

moby-live/Perl/MOBY/Adaptor/moby queryapi.pm,1.31,1.32
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi.pm,v
retrieving revision 1.31
retrieving revision 1.32
diff -u -r1.31 -r1.32
--- /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi.pm	2005/11/20 15:45:35	1.31
+++ /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi.pm	2007/01/30 14:57:47	1.32
@@ -1308,11 +1308,75 @@
 	die "get_relationship not implemented in adaptor\n";
 }
 
+=head2 get_all_relationships
+
+ Title     :	get_all_relationships
+ Usage     :	my $un = $API->get_all_relationships(%args)
+ Function  :	Execute a query for all relationships represented in $ontology_term2term
+ Args      :    direction    => String - direction in the ontology (either 'root' or 'leaves')
+ 		ontology     => String - name of the table ontology
+ Returns   :	reference to hash with the following structure:
+                $resultHash->{String relationship_type}->{Integer key_entity_id} = <VALUE>
+                The structure of <VALUE> depends on relationship_type and direction:
+                HAS/HASA    :
+                   <VALUE> = @([Integer value_entity_id, String articleName, Integer assertion_id])
+                ISA, leaves :
+                   <VALUE> = @(Integer value_entity_id)
+                ISA, root   :
+                   <VALUE> = Integer value_entity_id
+ Notes     :	The hash is built 'direction-aware', that is for
+                - root  : key_entity_id = ${ontology}1_id, value_entity_id = ${ontology}2_id
+                - leaves: key_entity_id = ${ontology}2_id, value_entity_id = ${ontology}1_id
+                The structure of the result hash is a bit complex because it is specifically
+                designed for usage by MOBY::OntolgyServer::Relationships
+                The result hash contains the entire table ${ontology}_term2term in order to
+                reduce DB interaction in the ontology exploration
+
+=cut
+
+# Get all relationships in the queried database in one go.  The
+# complete table ${ontology}_term2term is transferred into a hash
+# whose reference is finally returned.  Important: note that the hash
+# is built 'direction aware', that is for objects 'object1_id' is used
+# as key when direction is 'root' and 'object2_id' as value. Vice
+# versa for the 'leaves' direction.  Likewise for services.
+# Returns a hash reference.
+sub get_all_relationships{
+	die "get_all_relationships not implemented in adaptor\n";
+}
+
+=head2 get_deails_for_id_list
+
+ Title     :	get_deails_for_id_list
+ Usage     :	my $un = $API->get_all_relationships($ontology, $field_list, $id_list)
+ Function  :	Retrieve details specified in @$field_list from $ontology for ids in @$id_list
+ Args      :    $ontology   => String - name of the table ontology
+                $field_list => Reference to array of Strings representing table fields in $ontology
+                $id_list    => Reference to array of Integers representing ${ontology}_ids
+ Returns   :	reference to hash with the following structure:
+                $resultHash->{Integer ${ontology}_id}->{String field_name} = field_value
+ Notes     :    This function is generic with respect to which details (fields) are retrieved, but
+                is restricted to those tables whose name is identical to the ontology name (i.e.
+                currently 'object', 'service', 'namespace' and 'relationship')
+                Makes use of the 'select ... from ... where ... in (<LIST>)' statement syntax
+                in order to reduce the number of DB interactions
+                Used in MOBY::OntologyServer::Relationships, but maybe useful for other purposes...
+
+=cut
+  
+# retrieve details for a number of entities from table $ontology
+# represented by a list of ${ontology}_id's;
+# used in MOBY::OntologyServer::Relationships
+sub get_details_for_id_list {
+        die "get_details_for_id_list not implemented in adaptor\n";
+}
+
+
 # Not quite sure what this does...
 sub _checkURI {
 	die "_checkURI not implemented in adaptor\n";
 }
-
+  
 sub _dump {
 	my ($self) = @_;
     foreach my $attrname ( $self->_standard_keys ) {