Merge pull request #47 from linkml/issue-46

issue 46

Author: cmungall

docs/tutorial/pizza01-toppings-model.yaml

@@ -27,6 +27,7 @@ classes:
         slot_uri: rdfs:label
       conforms_to:
         name: conforms_to
+        range: string
         annotations:
           owl.fstring: AnnotationAssertion( dcterms:conformsTo {id} pizza:{V} )
         slot_uri: dcterms:conformsTo

linkml_owl/dumpers/owl_dumper.py

@@ -33,7 +33,7 @@
     SubObjectPropertyOf, TransitiveObjectProperty, SymmetricObjectProperty, AsymmetricObjectProperty, \
     ReflexiveObjectProperty, IrreflexiveObjectProperty, Annotation, ObjectMinCardinality, ObjectHasValue, \
     NamedIndividual, DataSomeValuesFrom, DataHasValue, DataAllValuesFrom, AnnotationProperty, DataProperty, Datatype, \
-    DisjointClasses, DisjointUnion
+    DisjointClasses, DisjointUnion, DataPropertyAssertion
 
 from linkml_runtime.dumpers.dumper_root import Dumper
 from linkml_runtime.utils.yamlutils import YAMLRoot
@@ -210,10 +210,23 @@ def transform(self, element: YAMLRoot, schema: SchemaDefinition, is_element_an_o
         if element is None:
             return None
         try:
-            # translate Enum
+            # naive method to test if an object is an enum:
+            # try accessing the `meaning` field. If this fails,
+            # an exception is thrown, and we carry on.
+            # (when owl_duper is refactored to not be dependent on
+            #  python dataclasses this will no longer be necessary)
             meaning = element.meaning
-            return self._get_IRI_str(meaning)
+            if is_element_an_object:
+                # enum is used in an object context: translate to URI
+                if not meaning:
+                    enum_uri = schema.default_prefix + ":" + type(element).__name__
+                    meaning = enum_uri + "#" + str(element).replace(" ", "+")
+                return self._get_IRI_str(meaning)
+            else:
+                # enum is used in a data context - stringify
+                return str(element)
         except AttributeError:
+            # not an enum - carry on
             pass
         if not self._instance_of_linkml_class(element):
             # TODO: better way of detecting atoms
@@ -324,6 +337,8 @@ def transform(self, element: YAMLRoot, schema: SchemaDefinition, is_element_an_o
             slot_interps = self._get_slot_interpretations(slot, linkml_class_name)
             logging.debug(f'OWL interpretations for {k}={slot_interps}')
             is_object_ref = slot.range in self.schema.classes
+            if "ObjectPropertyAssertion" in slot_interps or "ObjectProperty" in slot_interps:
+                is_object_ref = True
             # normalize input_vals to a list, then recursively transform
             if isinstance(v, list):
                 input_vals = v
@@ -390,7 +405,7 @@ def transform(self, element: YAMLRoot, schema: SchemaDefinition, is_element_an_o
             #    eai.add_operands((0, SubClassOf.__name__, ObjectUnionOf.__name__), parents, axiom_annotations)
             axiom_type = None
             # TODO: make this more generic / less repetitive
-            axiom_types = [SubClassOf, SubObjectPropertyOf, ClassAssertion, ObjectPropertyAssertion, EquivalentClasses, InverseObjectProperties,ObjectPropertyDomain, ObjectPropertyRange, AnnotationAssertion]
+            axiom_types = [SubClassOf, SubObjectPropertyOf, ClassAssertion, ObjectPropertyAssertion, DataPropertyAssertion, EquivalentClasses, InverseObjectProperties,ObjectPropertyDomain, ObjectPropertyRange, AnnotationAssertion]
             for candidate_axiom_type in axiom_types:
                 if candidate_axiom_type.__name__ in slot_interps:
                     axiom_type = candidate_axiom_type
@@ -445,6 +460,8 @@ def transform(self, element: YAMLRoot, schema: SchemaDefinition, is_element_an_o
                         axiom = ClassAssertion(parent, subj)
                     elif axiom_type == ObjectPropertyAssertion:
                         axiom = ObjectPropertyAssertion(slot_uri, subj, parent)
+                    elif axiom_type == DataPropertyAssertion:
+                        axiom = DataPropertyAssertion(slot_uri, subj, parent)
                     elif axiom_type == InverseObjectProperties:
                         axiom = InverseObjectProperties(subj, parent)
                     elif axiom_type == ObjectPropertyDomain:

poetry.lock

@@ -39,7 +39,7 @@ python = "^3.8.1"
 click = "*"
 funowl = ">=0.2.3"
 Jinja2 = ">=3.0.3"
-linkml = ">=1.7.4"
+linkml = "^1.7.10"
 linkml-runtime = ">=1.7.0"
 
 [tool.poetry.dev-dependencies]

pyproject.toml

@@ -0,0 +1,42 @@
+id: http://example.org/enum-test
+name: enum-test
+imports:
+  - linkml:types
+prefixes:
+  linkml: https://w3id.org/linkml/
+  ex: http://example.org/enum-test/
+  BFO: http://purl.obolibrary.org/obo/BFO_
+
+default_prefix: ex
+default_curi_maps:
+  - semweb_context
+
+slots:
+  id:
+    identifier: true
+    range: uriorcurie
+  job:
+    range: JobEnum
+    annotations:
+      owl: ObjectPropertyAssertion
+
+  job_str:
+    range: JobEnum
+    annotations:
+      owl: DataPropertyAssertion
+
+classes:
+
+  Person:
+    slots:
+      - id
+      - job
+      - job_str
+
+enums:
+  JobEnum:
+    permissible_values:
+      Bricklayer:
+      Chimney Sweep:
+      Welder:
+        meaning: ex:Welder

tests/inputs/enum_model.yaml

@@ -19,9 +19,23 @@ Ontology( <https://w3id.org/cmungall/monsters-and-magic>
     SubClassOf( mnm:Humanoid mnm:Creature )
     Declaration( Class( mnm:Orc ) )
     AnnotationAssertion( schema:description mnm:Orc "An orc is a humanoid creature from Middle-earth." )
+    DataPropertyAssertion( mnm:armor_class mnm:Orc "13"^^xsd:integer )
+    DataPropertyAssertion( mnm:strength mnm:Orc "16"^^xsd:integer )
+    DataPropertyAssertion( mnm:dexterity mnm:Orc "11"^^xsd:integer )
+    DataPropertyAssertion( mnm:constitution mnm:Orc "12"^^xsd:integer )
+    DataPropertyAssertion( mnm:intelligence mnm:Orc "10"^^xsd:integer )
+    DataPropertyAssertion( mnm:wisdom mnm:Orc "8"^^xsd:integer )
+    DataPropertyAssertion( mnm:charisma mnm:Orc "8"^^xsd:integer )
     SubClassOf( mnm:Orc mnm:Humanoid )
     Declaration( Class( mnm:Goblin ) )
     AnnotationAssertion( schema:description mnm:Goblin "A goblin is a humanoid creature from Middle-earth." )
+    DataPropertyAssertion( mnm:armor_class mnm:Goblin "15"^^xsd:integer )
+    DataPropertyAssertion( mnm:strength mnm:Goblin "8"^^xsd:integer )
+    DataPropertyAssertion( mnm:dexterity mnm:Goblin "14"^^xsd:integer )
+    DataPropertyAssertion( mnm:constitution mnm:Goblin "10"^^xsd:integer )
+    DataPropertyAssertion( mnm:intelligence mnm:Goblin "10"^^xsd:integer )
+    DataPropertyAssertion( mnm:wisdom mnm:Goblin "8"^^xsd:integer )
+    DataPropertyAssertion( mnm:charisma mnm:Goblin "8"^^xsd:integer )
     SubClassOf( mnm:Goblin mnm:Humanoid )
     Declaration( Class( mnm:SerpentineCreature ) )
     AnnotationAssertion( schema:description mnm:SerpentineCreature "A serpentine creature is a creature that has a snake-like body." )
@@ -67,24 +81,66 @@ Ontology( <https://w3id.org/cmungall/monsters-and-magic>
     SubClassOf( mnm:MagicallyCreatedCreature mnm:Creature )
     Declaration( Class( mnm:RugOfSmothering ) )
     AnnotationAssertion( schema:description mnm:RugOfSmothering "A rug of smothering is a rug that can be used to suffocate a creature." )
+    DataPropertyAssertion( mnm:armor_class mnm:RugOfSmothering "13"^^xsd:integer )
+    DataPropertyAssertion( mnm:strength mnm:RugOfSmothering "16"^^xsd:integer )
+    DataPropertyAssertion( mnm:dexterity mnm:RugOfSmothering "11"^^xsd:integer )
+    DataPropertyAssertion( mnm:constitution mnm:RugOfSmothering "12"^^xsd:integer )
+    DataPropertyAssertion( mnm:intelligence mnm:RugOfSmothering "10"^^xsd:integer )
+    DataPropertyAssertion( mnm:wisdom mnm:RugOfSmothering "8"^^xsd:integer )
+    DataPropertyAssertion( mnm:charisma mnm:RugOfSmothering "8"^^xsd:integer )
     SubClassOf( mnm:RugOfSmothering mnm:MagicallyCreatedCreature )
     Declaration( Class( mnm:Basilisk ) )
     AnnotationAssertion( schema:description mnm:Basilisk "A basilisk is a legendary serpent-like creature with the body of a snake and the head of a king cobra." )
+    DataPropertyAssertion( mnm:armor_class mnm:Basilisk "13"^^xsd:integer )
+    DataPropertyAssertion( mnm:strength mnm:Basilisk "16"^^xsd:integer )
+    DataPropertyAssertion( mnm:dexterity mnm:Basilisk "11"^^xsd:integer )
+    DataPropertyAssertion( mnm:constitution mnm:Basilisk "12"^^xsd:integer )
+    DataPropertyAssertion( mnm:intelligence mnm:Basilisk "10"^^xsd:integer )
+    DataPropertyAssertion( mnm:wisdom mnm:Basilisk "8"^^xsd:integer )
+    DataPropertyAssertion( mnm:charisma mnm:Basilisk "8"^^xsd:integer )
     SubClassOf( mnm:Basilisk mnm:SerpentineCreature )
     Declaration( Class( mnm:UndeadCreature ) )
     AnnotationAssertion( schema:description mnm:UndeadCreature "An undead creature is a creature that is dead, but has been brought back to life by magic." )
     SubClassOf( mnm:UndeadCreature mnm:Humanoid )
     Declaration( Class( mnm:WhiteWalker ) )
     AnnotationAssertion( schema:description mnm:WhiteWalker "A white walker is an undead creature from the Game of Thrones universe." )
+    DataPropertyAssertion( mnm:armor_class mnm:WhiteWalker "13"^^xsd:integer )
+    DataPropertyAssertion( mnm:strength mnm:WhiteWalker "16"^^xsd:integer )
+    DataPropertyAssertion( mnm:dexterity mnm:WhiteWalker "11"^^xsd:integer )
+    DataPropertyAssertion( mnm:constitution mnm:WhiteWalker "12"^^xsd:integer )
+    DataPropertyAssertion( mnm:intelligence mnm:WhiteWalker "10"^^xsd:integer )
+    DataPropertyAssertion( mnm:wisdom mnm:WhiteWalker "8"^^xsd:integer )
+    DataPropertyAssertion( mnm:charisma mnm:WhiteWalker "8"^^xsd:integer )
     SubClassOf( mnm:WhiteWalker mnm:UndeadCreature )
     Declaration( Class( mnm:Lich ) )
     AnnotationAssertion( schema:description mnm:Lich "A lich is a fictional undead creature in the Dungeons & Dragons fantasy role-playing game." )
+    DataPropertyAssertion( mnm:armor_class mnm:Lich "13"^^xsd:integer )
+    DataPropertyAssertion( mnm:strength mnm:Lich "16"^^xsd:integer )
+    DataPropertyAssertion( mnm:dexterity mnm:Lich "11"^^xsd:integer )
+    DataPropertyAssertion( mnm:constitution mnm:Lich "12"^^xsd:integer )
+    DataPropertyAssertion( mnm:intelligence mnm:Lich "10"^^xsd:integer )
+    DataPropertyAssertion( mnm:wisdom mnm:Lich "8"^^xsd:integer )
+    DataPropertyAssertion( mnm:charisma mnm:Lich "8"^^xsd:integer )
     SubClassOf( mnm:Lich mnm:UndeadCreature )
     Declaration( Class( mnm:Vampire ) )
     AnnotationAssertion( schema:description mnm:Vampire "A vampire is a fictional undead creature in the Dungeons & Dragons fantasy role-playing game." )
+    DataPropertyAssertion( mnm:armor_class mnm:Vampire "13"^^xsd:integer )
+    DataPropertyAssertion( mnm:strength mnm:Vampire "16"^^xsd:integer )
+    DataPropertyAssertion( mnm:dexterity mnm:Vampire "11"^^xsd:integer )
+    DataPropertyAssertion( mnm:constitution mnm:Vampire "12"^^xsd:integer )
+    DataPropertyAssertion( mnm:intelligence mnm:Vampire "10"^^xsd:integer )
+    DataPropertyAssertion( mnm:wisdom mnm:Vampire "8"^^xsd:integer )
+    DataPropertyAssertion( mnm:charisma mnm:Vampire "8"^^xsd:integer )
     SubClassOf( mnm:Vampire mnm:UndeadCreature )
     Declaration( Class( mnm:Zombie ) )
     AnnotationAssertion( schema:description mnm:Zombie "A zombie is a fictional undead creature in the Dungeons & Dragons fantasy role-playing game." )
+    DataPropertyAssertion( mnm:armor_class mnm:Zombie "13"^^xsd:integer )
+    DataPropertyAssertion( mnm:strength mnm:Zombie "16"^^xsd:integer )
+    DataPropertyAssertion( mnm:dexterity mnm:Zombie "11"^^xsd:integer )
+    DataPropertyAssertion( mnm:constitution mnm:Zombie "12"^^xsd:integer )
+    DataPropertyAssertion( mnm:intelligence mnm:Zombie "10"^^xsd:integer )
+    DataPropertyAssertion( mnm:wisdom mnm:Zombie "8"^^xsd:integer )
+    DataPropertyAssertion( mnm:charisma mnm:Zombie "8"^^xsd:integer )
     SubClassOf( mnm:Zombie mnm:UndeadCreature )
     Declaration( NamedIndividual( mnm:Smaug ) )
     Declaration( Class( mnm:Smaug ) )
@@ -98,6 +154,7 @@ Ontology( <https://w3id.org/cmungall/monsters-and-magic>
     ClassAssertion( mnm:WhiteWalker mnm:TheNightKing )
     Declaration( Class( mnm:Paladin ) )
     AnnotationAssertion( schema:description mnm:Paladin "A paladin is a holy warrior who fights evil using divine magic." )
+    DataPropertyAssertion( mnm:hit_dice mnm:Paladin "D10" )
     Declaration( Class( mnm:Wizard ) )
     AnnotationAssertion( schema:description mnm:Wizard "A wizard is a person who practices magic." )
     Declaration( Class( mnm:Rogue ) )