Merge pull request #31 from linkml/singleton-intersections

Comvert singleton IntersectionOf(X) into X.

.github/workflows/main.yaml

@@ -31,10 +31,7 @@ jobs:
       #          install & configure poetry         
       #----------------------------------------------
       - name: Install Poetry
-        uses: snok/install-poetry@v1.1.1
-        with:
-          virtualenvs-create: true
-          virtualenvs-in-project: true      
+        uses: snok/install-poetry@v1.3.1
 
       #----------------------------------------------
       #       load cached venv if cache exists      

linkml_owl/dumpers/owl_dumper.py

@@ -5,6 +5,7 @@
 
 import click
 from funowl.converters.functional_converter import to_python
+from funowl.writers.FunctionalWriter import FunctionalWriter
 from jinja2 import Template
 from linkml.generators.pythongen import PythonGenerator
 from linkml_runtime import SchemaView
@@ -233,7 +234,7 @@ def transform(self, element: YAMLRoot, schema: SchemaDefinition, is_element_an_o
         for fstr in self._get_inferred_class_annotations(c, 'owl.fstring'):
             self.add_axioms_from_fstring(fstr, element)
         for tmpl_str in self._get_inferred_class_annotations(c, 'owl.template'):
-            self.add_axioms_from_template(tmpl_str, element)
+            self.add_axioms_from_template(tmpl_str, element, schema=schema)
         cls_interps = self._get_class_interpretations(c)
         subj = None
         eai = EntityAxiomIndex()
@@ -272,6 +273,8 @@ def transform(self, element: YAMLRoot, schema: SchemaDefinition, is_element_an_o
                 # the role of the identifier slot is to determine the IRI for the element;
                 # it generates no axioms of its own
                 continue
+            if 'owl.ignore' in slot.annotations:
+                continue
             schema_level_slot = self._get_schema_level_slot(slot)
             # lookup OWL settings on each slot
             owl_templates = self._get_inferred_slot_annotations(slot, 'owl.template', linkml_class_name)
@@ -440,18 +443,30 @@ def transform(self, element: YAMLRoot, schema: SchemaDefinition, is_element_an_o
         # all per-slot axioms have been processed; axioms that span
         # multiple slots are now processed
         if "IntersectionOf" in cls_interps:
+            if len(unprocessed_parents) == 0:
+                raise ValueError(f"Cannot process IntersectionOf with no parents for {element}")
+            if len(unprocessed_parents) == 1:
+                logging.debug(f"Simplifying IntersectionOf(...) to {unprocessed_parents[0]}")
+                return unprocessed_parents[0]
             expr = ObjectIntersectionOf(*unprocessed_parents)
             logging.debug(f"Returning expression {expr} // {eai.operand_list_index.items()}")
             return expr
         for op_key, operands in eai.operand_list_index.items():
             _, interp, operator = op_key
             logging.debug(f'EntityAxiomIndex {subj}: {interp} => {operator} over {operands}')
-            if len(operands) < 2:
+            if len(operands) == 0:
                 raise ValueError(f'Too few operands: {operands} for {operator} in {subj}')
-            if operator == ObjectUnionOf.__name__:
+            if len(operands) == 1:
+                logging.debug(f"Simplifying {operator}(...) to {operands[0]}")
+                return operands[0]
+            elif operator == ObjectUnionOf.__name__:
                 expr = ObjectUnionOf(*operands)
             elif operator == ObjectIntersectionOf.__name__:
-                expr = ObjectIntersectionOf(*operands)
+                if len(operands) == 1:
+                    logging.debug(f"Simplifying IntersectionOf(...) to {operands[0]}")
+                    expr = operands[0]
+                else:
+                    expr = ObjectIntersectionOf(*operands)
             else:
                 raise ValueError(f'Cannot handle operator: {operator}')
             if interp == EquivalentClasses.__name__:
@@ -652,13 +667,24 @@ def add_axioms_from_fstring(self, fstring: Union[str, meta.Annotation], element:
         logging.debug(f'AXIOMS >> = {axioms}')
         self.ontology.axioms += axioms
 
-    def add_axioms_from_template(self, template_ann: Union[str, meta.Annotation], element: YAMLRoot, val: Any = None):
+    def add_axioms_from_template(self, template_ann: Union[str, meta.Annotation], element: YAMLRoot, val: Any = None, schema: SchemaDefinition = None):
         # TODO: simplify, change arg to str
         d = self._element_to_template_dict(element, val)
         if isinstance(template_ann, str):
             tstr = template_ann
         else:
             tstr = template_ann.value
+        def tr(e: YAMLRoot):
+            expr = self.transform(e, schema=schema, is_element_an_object=False)
+            fw = FunctionalWriter()
+            logging.debug(f"template.transform({e}) DIRECT = {expr}")
+            owl_str = str(expr.to_functional(fw))
+            logging.debug(f"template.transform({e}) = {owl_str}")
+            return owl_str
+        if "tr" in d:
+            d["_tr"] = tr
+        else:
+            d["tr"] = tr
         jt = Template(tstr)
         owl_str = jt.render(**d)
         axioms = self.parse_axioms_string(owl_str).ontology.axioms
@@ -750,8 +776,11 @@ def cli(inputfile: str, schema: str, target_class, module, output, format, autof
     if autofill:
         dumper.autofill = True
     doc = dumper.dumps(element, schemaview=sv)
-    with open(output, 'w') as stream:
-        stream.write(str(doc))
+    if output is None:
+        print(str(doc))
+    else:
+        with open(output, 'w') as stream:
+            stream.write(str(doc))
 
 
 if __name__ == '__main__':

tests/inputs/owl_dumper_test.yaml

@@ -13,6 +13,7 @@ prefixes:
   PATO: http://purl.obolibrary.org/obo/PATO_
   skos: http://www.w3.org/2004/02/skos/core#
   dcterms: http://purl.org/dc/terms/
+  schema: http://schema.org/
   x: http://example.org/
 
 default_prefix: test
@@ -299,6 +300,15 @@ classes:
           owl: ObjectSomeValuesFrom
     annotations:
       owl: Class
+  HasName:
+    is_a: NamedThing
+    description: test metaclass illustrating data has value from
+    attributes:
+      has_name:
+        required: true
+        slot_uri: schema:name
+        annotations:
+          owl: DataHasValue
   EquivGenusAndPartOf:
     is_a: NamedThing
     description: test metaclass illustrating basic simple genus-differentia style logical definition, including so-called hidden GCIs

tests/inputs/recipe.data.yaml

@@ -0,0 +1,101 @@
+url: http://example.org
+label: Simple Spaghetti
+description: A classic spaghetti recipe made with onion, bell peppers, garlic powder,
+  butter, salt, pepper, tomato sauce, and hamburger meat.
+categories:
+- AUTO:Main%20dish
+- HANCESTRO:0307
+ingredients:
+- food_item:
+    food: AUTO:Small%20onion
+    state: chopped
+  amount:
+    value: '1'
+    unit: AUTO:cup
+- food_item:
+    food: FOODON:00003485
+    state: chopped
+  amount:
+    value: chopped
+    unit: AUTO:N/A
+- food_item:
+    food: FOODON:00003582
+    state: powder
+- food_item:
+    food: FOODON:03310351
+- food_item:
+    food: AUTO:salt
+- food_item:
+    food: FOODON:00001649
+- food_item:
+    food: FOODON:03301217
+    state: canned
+  amount:
+    value: '2'
+    unit: AUTO:cans
+- food_item:
+    food: AUTO:16-ounce%20box%20spaghetti%20noodles
+    state: chopped, diced
+  amount:
+    value: '1'
+- food_item:
+    food: FOODON:00001282
+    state: chopped/diced
+  amount:
+    value: "1-1 1\u20442"
+    unit: AUTO:lb
+steps:
+- action: AUTO:melt%3B%20saut%C3%A9
+  inputs:
+  - food: FOODON:03310351
+  - food: FOODON:03301704
+  - food: AUTO:bell%20peppers
+    state: chopped
+  utensils:
+  - AUTO:pan
+- action: AUTO:add%3B%20cook
+  inputs:
+  - food: FOODON:00001282
+    state: chopped/diced
+  outputs:
+  - food: AUTO:meat
+    state: well done
+  utensils:
+  - AUTO:pan
+- action: AUTO:add%3B
+  inputs:
+  - food: FOODON:03000227
+    state: sauce
+  - food: AUTO:salt
+  - food: FOODON:00001649
+  - food: FOODON:00003582
+    state: powder
+  utensils:
+  - AUTO:n/a
+- action: AUTO:adjust%3B
+  inputs:
+  - food: AUTO:salt
+  - food: FOODON:00001649
+  - food: FOODON:00003582
+    state: powder
+  outputs:
+  - food: AUTO:adjusted
+    state: to own tastes
+  utensils:
+  - AUTO:none
+- action: AUTO:cook
+  inputs:
+  - food: AUTO:noodles
+  outputs:
+  - food: AUTO:noodles
+  utensils:
+  - AUTO:pan
+- action: AUTO:mix%3B
+  inputs:
+  - food: FOODON:03311146
+  - food: AUTO:noodles
+  outputs:
+  - food: FOODON:03311146
+  - food: AUTO:noodles
+  utensils:
+  - AUTO:none