Support for enum mapping for slots with multiple enum ranges

.github/CODE_OF_CONDUCT.md

@@ -5,7 +5,7 @@
 We as members, contributors, and leaders pledge to make participation in our
 community a harassment-free experience for everyone, regardless of age, body
 size, visible or invisible disability, ethnicity, sex characteristics, gender
-identity and expression, level of experience, education, socio-economic status,
+identity and expression, level of experience, education, socioeconomic status,
 nationality, personal appearance, race, caste, color, religion, or sexual
 identity and orientation.
 

src/linkml_map/transformer/object_transformer.py

@@ -181,10 +181,15 @@ def map_object(
                 elif target_type == "curie":
                     return self.compress_uri(source_obj)
             return source_obj
-        if source_type in sv.all_enums():
-            # TODO: enum derivations
-            return self.transform_enum(source_obj, source_type, source_obj)
-            # return str(source_obj)
+
+        # Do enumeration transform if source_type has enumeration name(s)
+        source_type_enums = yaml.safe_load(source_type)
+        if not isinstance(source_type_enums, list):
+            source_type_enums = [source_type_enums]
+        source_type_enums = [enum for enum in source_type_enums if enum in sv.all_enums()]
+        if len(source_type_enums) > 0:
+            return self.transform_enum(source_obj, source_type_enums, source_obj)
+
         source_obj_typed = None
         if isinstance(source_obj, (BaseModel, YAMLRoot)):
             # ensure dict
@@ -424,24 +429,28 @@ def transform_object(
         tr_obj_dict = self.map_object(source_obj, source_type_name)
         return target_class(**tr_obj_dict)
 
-    def transform_enum(self, source_value: str, enum_name: str, source_obj: Any) -> Optional[str]:
-        enum_deriv = self._get_enum_derivation(enum_name)
-        if enum_deriv.expr:
-            try:
-                if enum_deriv.expr:
-                    v = eval_expr(enum_deriv.expr, **source_obj, NULL=None)
-            except Exception:
-                aeval = Interpreter(usersyms={"src": source_obj, "target": None})
-                aeval(enum_deriv.expr)
-                v = aeval.symtable["target"]
-            if v is not None:
-                return v
-        for pv_deriv in enum_deriv.permissible_value_derivations.values():
-            if source_value == pv_deriv.populated_from:
-                return pv_deriv.name
-            if source_value in pv_deriv.sources:
-                return pv_deriv.name
-        if enum_deriv.mirror_source:
-            return str(source_value)
-        else:
-            return None
+    def transform_enum(
+        self, source_value: str, enum_name: Union[str, List[str]], source_obj: Any
+    ) -> Optional[str]:
+        if isinstance(enum_name, str):
+            enum_name = [enum_name]
+        for cur_enum in enum_name:
+            enum_deriv = self._get_enum_derivation(cur_enum)
+            if enum_deriv.expr:
+                try:
+                    if enum_deriv.expr:
+                        v = eval_expr(enum_deriv.expr, **source_obj, NULL=None)
+                except Exception:
+                    aeval = Interpreter(usersyms={"src": source_obj, "target": None})
+                    aeval(enum_deriv.expr)
+                    v = aeval.symtable["target"]
+                if v is not None:
+                    return v
+            for pv_deriv in enum_deriv.permissible_value_derivations.values():
+                if source_value == pv_deriv.populated_from:
+                    return pv_deriv.name
+                if source_value in pv_deriv.sources:
+                    return pv_deriv.name
+            if enum_deriv.mirror_source:
+                return str(source_value)
+        return None

tests/input/examples/multi_enum/data/Container-001.yaml

@@ -0,0 +1,21 @@
+lights:
+  - colors:
+    - light_red
+    - dark_green
+    - dark_blue
+    - light_magenta
+    - not_available
+    main_color: dark_green
+    mirror_test_slot: light_red
+  - colors:
+    - light_green
+    main_color: light_green
+    mirror_test_slot: light_magenta
+  - colors:
+    - other
+    main_color: other
+    mirror_test_slot: dark_purple
+  - colors:
+    - light_blue
+    main_color: light_blue
+    mirror_test_slot: not_available

tests/input/examples/multi_enum/output/Container-001.transformed.yaml

@@ -0,0 +1,21 @@
+lights_inventory:
+- light_colors:
+  - red
+  - green
+  - blue
+  - magenta
+  - na
+  light_main_color: green
+  mirror_test_slot: red
+- light_colors:
+  - green
+  light_main_color: green
+  mirror_test_slot: magenta
+- light_colors:
+  - oth
+  light_main_color: oth
+  mirror_test_slot: purple
+- light_colors:
+  - blue
+  light_main_color: blue
+  mirror_test_slot: not_available

tests/input/examples/multi_enum/source/lights.yaml

@@ -0,0 +1,65 @@
+name: light_bulbs
+id: light_bulbs
+description: Light Bulbs
+imports:
+- linkml:types
+default_range: string
+enums:
+  primary_colors:
+    permissible_values:
+      light_red:
+      dark_red:
+      light_green:
+      dark_green:
+      light_blue:
+      dark_blue:
+  secondary_colors:
+    permissible_values:
+      light_cyan:
+      dark_cyan:
+      light_magenta:
+      dark_magenta:
+      light_yellow:
+      dark_yellow:
+  mirror_test_colors:
+    permissible_values:
+      dark_purple:
+      dark_turquoise:
+      dark_fuchsia:
+  missingness:
+    permissible_values:
+      not_available:
+      other:
+classes:
+  lights:
+    slots:
+      - colors
+      - main_color
+      - mirror_test_slot
+  Container:
+    tree_root: True
+    attributes:
+      lights:
+        range: lights
+        multivalued: True
+        inlined_as_list: True
+slots:
+    colors:
+      range:
+        - primary_colors
+        - secondary_colors
+        - missingness
+      multivalued: True
+      inlined_as_list: True
+    main_color:
+      range:
+        - primary_colors
+        - secondary_colors
+        - missingness
+      multivalued: False
+    mirror_test_slot:
+      range:
+        - primary_colors
+        - secondary_colors
+        - mirror_test_colors
+        - missingness

tests/input/examples/multi_enum/target/lights_inventory.yaml

@@ -0,0 +1,61 @@
+name: light_bulbs_simple
+id: light_bulbs_simple
+description: Light Bulbs (Simplified)
+imports:
+- linkml:types
+default_range: string
+enums:
+  light_size_enum:
+    permissible_values:
+      size_0:
+      size_1:
+      size_2:
+  light_primary_colors_enum:
+    permissible_values:
+      red:
+      green:
+      blue:
+  light_secondary_colors_enum:
+    permissible_values:
+      cyan:
+      magenta:
+      yellow:
+  missingness_enum:
+    permissible_values:
+      na:
+      oth:
+classes:
+  lights_inventory:
+    slots:
+      - light_sizes
+      - light_colors
+      - light_mirror_test_slot
+  Container:
+    tree_root: True
+    attributes:
+      all_lights:
+        range: lights_inventory
+        multivalued: True
+        inlined_as_list: True
+slots:
+    light_sizes:
+      range:
+        - light_size_enum
+        - missingness_enum
+      multivalued: True
+      inlined_as_list: True
+    light_colors:
+      range: 
+        - light_primary_colors_enum
+        - light_secondary_colors_enum
+        - missingness_enum
+      multivalued: True
+      inlined_as_list: True
+    light_main_color:
+      range: 
+        - light_primary_colors_enum
+        - light_secondary_colors_enum
+        - missingness_enum
+      multivalued: False
+    light_mirror_test_slot:
+      range: string

tests/input/examples/multi_enum/transform/lights_to_lights_simple.transform.yaml

@@ -0,0 +1,90 @@
+class_derivations:
+  lights_inventory:
+    name: lights_inventory
+    populated_from: lights
+    slot_derivations:
+      light_colors:
+        name: light_colors
+        populated_from: colors
+      light_main_color:
+        name: light_main_color
+        populated_from: main_color
+      light_mirror_test_slot:
+        name: mirror_test_slot
+        populated_from: mirror_test_slot
+  Container:
+    name: Container
+    slot_derivations:
+      lights_inventory:
+        populated_from: lights
+        range: string
+enum_derivations:
+  missingness_enum:
+    name: missingness_enum
+    mirror_source: false
+    populated_from: missingness
+    permissible_value_derivations:
+      na:
+        name: na
+        populated_from: not_available
+      oth:
+        name: oth
+        populated_from: other
+  light_primary_colors_enum:
+    name: light_primary_colors_enum
+    mirror_source: false
+    populated_from: primary_colors
+    permissible_value_derivations:
+      red:
+        name: red
+        sources:
+        - light_red
+        - dark_red
+      green:
+        name: green
+        sources:
+        - light_green
+        - dark_green
+      blue:
+        name: blue
+        sources:
+        - light_blue
+        - dark_blue
+  light_secondary_colors_enum:
+    name: light_secondary_colors_enum
+    mirror_source: false
+    populated_from: secondary_colors
+    permissible_value_derivations:
+      cyan:
+        name: cyan
+        sources:
+        - light_cyan
+        - dark_cyan
+      magenta:
+        name: magenta
+        sources:
+        - light_magenta
+        - dark_magenta
+      yellow:
+        name: yellow
+        sources:
+        - light_yellow
+        - dark_yellow
+  light_test_colors_enum:
+    # This derivation is for testing mirror_source=True. When transforming a slot with multiple enumerations in the range,
+    # and we encounter an enum derivation with mirror_source=True, then if no permissible value derivation is matched we return
+    # the source value unchanged, and ignore any further enum derivations.
+    name: light_test_colors_enum
+    mirror_source: true
+    populated_from: mirror_test_colors
+    permissible_value_derivations:
+      purple:
+        name: purple
+        populated_from: dark_purple
+      turquoise:
+        name: turquoise
+        populated_from: dark_turquoise
+      fuchsia:
+        name: fuchsia
+        populated_from: dark_fuchsia
+

tests/test_transformer/test_transformer_examples.py

@@ -9,6 +9,7 @@
     "personinfo_basic",
     "type_coercion",
     "biolink",
+    "multi_enum",
 ]