Merge pull request #207 from emmo-repo/issue183_function_add_class

Added function new_entity to ontology

emmo/ontology.py

@@ -14,6 +14,7 @@
 import warnings
 import uuid
 import tempfile
+import types
 from collections import defaultdict
 
 import rdflib
@@ -1003,14 +1004,25 @@ def addancestors(e, n, s):
             return ancestors
 
     def get_wu_palmer_measure(self, cls1, cls2):
-        '''
-        Returns the Wu Palmer measure for semantic similarity between
+        """ Return Wu-Palmer measure for semantic similarity.
+
+        Returns Wu-Palmer measure for semantic similarity between
         two concepts.
         Wu, Palmer; ACL 94: Proceedings of the 32nd annual meeting on
         Association for Computational Linguistics, June 1994.
-        '''
+        """
         cca = self.closest_common_ancestor(cls1, cls2)
         ccadepth = self.number_of_generations(cca, self.Thing)
         n1 = self.number_of_generations(cls1, cca)
         n2 = self.number_of_generations(cls2, cca)
         return 2 * ccadepth / (n1 + n2 + 2 * ccadepth)
+
+    def new_entity(self, name, parent):
+        """Create and return new entity
+
+        Makes a new entity in the ontology with given parent.
+        Return the new entity
+        """
+        with self:
+            e = types.new_class(name, (parent, ))
+        return e

emmo/tests/test_basic.py

@@ -20,27 +20,27 @@
 onto.imported_ontologies.append(emmo)
 onto.base_iri = 'http://emmo.info/examples/test#'
 
-with onto:
+# Add entity directly
+onto.new_entity('Hydrogen', emmo.Atom)
 
-    class Hydrogen(emmo.Atom):
-        pass
+with onto:
 
+    # Add entity using python classes
     class Oxygen(emmo.Atom):
         pass
 
     class H2O(emmo.Molecule):
         """Water molecule."""
-        emmo.hasSpatialDirectPart.exactly(2, Hydrogen)
+        emmo.hasSpatialDirectPart.exactly(2, onto.Hydrogen)
         emmo.hasSpatialDirectPart.exactly(1, Oxygen)
 
     # Create some
-    H1 = Hydrogen()
-    H2 = Hydrogen()
+    H1 = onto.Hydrogen()
+    H2 = onto.Hydrogen()
     O = Oxygen()  # noqa: E741
     w = H2O()
     w.hasSpatialDirectPart = [H1, H2,  O]
 
-
 onto.sync_attributes(name_policy='sequential', name_prefix='myonto_')
 assert onto.base_iri + 'myonto_0' in onto
 assert onto.base_iri + 'myonto_6' in onto
@@ -49,7 +49,6 @@ class H2O(emmo.Molecule):
 assert w.name.startswith('onto_')
 assert len(w.name) == 5 + 36
 
-
 # Remove all traces of onto such that they do not mess up other tests
 # when running pytest
 for e in itertools.chain(onto.classes(), onto.individuals()):