Merge pull request #37 from linkml/add-target_definition-to-data-model

Adding target_definition to model.

src/linkml_map/datamodel/transformer_model.yaml

@@ -17,12 +17,13 @@ description: |-
   - translation into another specification language, such as R2RML
 prefixes:
   linkml: https://w3id.org/linkml/
-  linkmltr: https://w3id.org/linkml/transformer/
+  linkmlmap: https://w3id.org/linkml/transformer/
   dcterms: http://purl.org/dc/terms/
   schema: http://schema.org/
   rdfs: http://www.w3.org/2000/01/rdf-schema#
   sh: http://www.w3.org/ns/shacl#
-default_prefix: linkmltr
+  STATO: http://purl.obolibrary.org/obo/STATO_
+default_prefix: linkmlmap
 
 imports:
   - linkml:types
@@ -178,6 +179,12 @@ classes:
         range: SlotDerivation
         multivalued: true
         inlined: true
+      target_definition:
+        range: Any
+        description: >-
+          LinkML class definition object for this slot.
+        comments:
+          - currently defined as Any to avoid coupling with metamodel
 
   AliasedClass:
     description: alias-class key value pairs for classes
@@ -228,12 +235,20 @@ classes:
         description: True if this is suppressed
       type_designator:
         range: boolean
+      target_definition:
+        range: Any
+        description: >-
+          LinkML definition object for this slot.
+        comments:
+          - currently defined as Any to avoid coupling with metamodel
       cast_collection_as:
         range: CollectionType
       dictionary_key:
         range: string
       stringification:
         range: StringificationConfiguration
+      aggregation_operation:
+        range: AggregationOperation
 
   EnumDerivation:
     is_a: ElementDerivation
@@ -330,6 +345,57 @@ classes:
       slot_name:
       class_name:
 
+  TransformationOperation:
+    abstract: true
+
+  AggregationOperation:
+    is_a: TransformationOperation
+    attributes:
+      operator:
+        range: AggregationType
+        required: true
+      null_handling:
+        range: InvalidValueHandlingStrategy
+      invalid_value_handling:
+        range: InvalidValueHandlingStrategy
+
+  GroupingOperation:
+    is_a: TransformationOperation
+    attributes:
+      null_handling:
+        range: InvalidValueHandlingStrategy
+
+  PivotOperation:
+    aliases:
+      - melt/unmelt
+      - reification/dereification
+    is_a: TransformationOperation
+    attributes:
+      direction:
+        range: PivotDirectionType
+        required: true
+      variable_slot:
+        aliases:
+          - var_name
+        range: SlotReference
+        ifabsent: string(variable)
+        description: Slot to use for the variable column in the melted/long representation.
+          In EAV this is the name of the 'A' variable
+      value_slot:
+        aliases:
+          - value_name
+        range: SlotReference
+        ifabsent: string(value)
+        description: Slot to use for the value column in the melted/long representation.
+          In EAV this is the name of the 'V' variable
+      unmelt_to_class:
+        description: In an unmelt operation, attributes (which are values in the long/melted/EAV
+          representation) must conform to valid attributes in this class
+        range: ClassReference
+      unmelt_to_slots:
+        range: SlotReference
+        multivalued: true
+
   KeyVal:
     attributes:
       key:
@@ -394,3 +460,46 @@ enums:
       JSON:
       YAML:
       TURTLE:
+  AggregationType:
+    permissible_values:
+      SUM:
+      AVERAGE:
+        aliases:
+          - mean
+          - avg
+        exact_mappings:
+          - STATO:0000230
+      COUNT:
+        exact_mappings:
+          - STATO:0000047
+      MIN:
+      MAX:
+      STD_DEV:
+        exact_mappings:
+          - STATO:0000237
+      VARIANCE:
+      MEDIAN:
+        exact_mappings:
+          - STATO:0000674
+      MODE:
+        exact_mappings:
+          - STATO:0000033
+      CUSTOM:
+      SET:
+      LIST:
+      ARRAY:
+  InvalidValueHandlingStrategy:
+    permissible_values:
+      IGNORE:
+      TREAT_AS_ZERO:
+      ERROR_OUT:
+  PivotDirectionType:
+    permissible_values:
+      MELT:
+        aliases:
+          - unpivot
+          - wide to long
+      UNMELT:
+        aliases:
+          - pivot
+          - long to wide

src/linkml_map/inference/schema_mapper.py

@@ -115,6 +115,18 @@ def _derive_class(self, class_derivation: ClassDerivation) -> ClassDefinition:
         for slot_derivation in class_derivation.slot_derivations.values():
             slot_definition = self._derive_slot(slot_derivation)
             target_class.attributes[slot_definition.name] = slot_definition
+        if class_derivation.is_a:
+            target_class.is_a = class_derivation.is_a
+        if class_derivation.mixins:
+            target_class.mixins = class_derivation.mixins
+        if class_derivation.target_definition:
+            spec_defn = ClassDefinition(
+                **{"name": target_class.name}, **class_derivation.target_definition
+            )
+            for k, v in vars(spec_defn).items():
+                curr_v = getattr(target_class, k, None)
+                if curr_v is None or curr_v == [] or curr_v == {}:
+                    setattr(target_class, k, v)
         self.source_to_target_class_mappings[populated_from].append(target_class.name)
         if class_derivation.overrides:
             curr = json_dumper.to_dict(target_class)
@@ -178,6 +190,12 @@ def _derive_slot(self, slot_derivation) -> SlotDefinition:
             target_slot.name = slot_derivation.name
         if slot_derivation.range:
             target_slot.range = slot_derivation.range
+        if slot_derivation.target_definition:
+            spec_defn = SlotDefinition(
+                **{"name": target_slot.name}, **slot_derivation.target_definition
+            )
+            for k, v in vars(spec_defn).items():
+                setattr(target_slot, k, v)
         if slot_derivation.unit_conversion:
             target_slot.unit = UnitOfMeasure(ucum_code=slot_derivation.unit_conversion.target_unit)
         if slot_derivation.stringification:

tests/input/examples/flattening/model/denormalized_model.py

@@ -17,9 +17,7 @@
 )
 from linkml_runtime.utils.metamodelcore import empty_list
 from linkml_runtime.utils.slot import Slot
-from linkml_runtime.utils.yamlutils import (
-    YAMLRoot,
-)
+from linkml_runtime.utils.yamlutils import YAMLRoot
 from rdflib import URIRef
 
 metamodel_version = "1.7.0"

tests/input/examples/flattening/model/normalized_model.py

@@ -17,10 +17,7 @@
 )
 from linkml_runtime.utils.metamodelcore import empty_dict, empty_list
 from linkml_runtime.utils.slot import Slot
-from linkml_runtime.utils.yamlutils import (
-    YAMLRoot,
-    extended_str,
-)
+from linkml_runtime.utils.yamlutils import YAMLRoot, extended_str
 from rdflib import URIRef
 
 metamodel_version = "1.7.0"

tests/input/examples/personinfo_basic/model/agent_model.py

@@ -12,26 +12,15 @@
 from typing import Any, ClassVar, Dict, List, Optional, Union
 
 from jsonasobj2 import as_dict
-from linkml_runtime.linkml_model.meta import (
-    EnumDefinition,
-    PermissibleValue,
-)
+from linkml_runtime.linkml_model.meta import EnumDefinition, PermissibleValue
 from linkml_runtime.utils.curienamespace import CurieNamespace
 from linkml_runtime.utils.dataclass_extensions_376 import (
     dataclasses_init_fn_with_kwargs,
 )
 from linkml_runtime.utils.enumerations import EnumDefinitionImpl
-from linkml_runtime.utils.metamodelcore import (
-    Bool,
-    XSDDate,
-    empty_dict,
-    empty_list,
-)
+from linkml_runtime.utils.metamodelcore import Bool, XSDDate, empty_dict, empty_list
 from linkml_runtime.utils.slot import Slot
-from linkml_runtime.utils.yamlutils import (
-    YAMLRoot,
-    extended_str,
-)
+from linkml_runtime.utils.yamlutils import YAMLRoot, extended_str
 from rdflib import URIRef
 
 metamodel_version = "1.7.0"

tests/input/examples/personinfo_basic/model/personinfo_model.py

@@ -12,26 +12,15 @@
 from typing import Any, ClassVar, Dict, List, Optional, Union
 
 from jsonasobj2 import as_dict
-from linkml_runtime.linkml_model.meta import (
-    EnumDefinition,
-    PermissibleValue,
-)
+from linkml_runtime.linkml_model.meta import EnumDefinition, PermissibleValue
 from linkml_runtime.utils.curienamespace import CurieNamespace
 from linkml_runtime.utils.dataclass_extensions_376 import (
     dataclasses_init_fn_with_kwargs,
 )
 from linkml_runtime.utils.enumerations import EnumDefinitionImpl
-from linkml_runtime.utils.metamodelcore import (
-    Bool,
-    XSDDate,
-    empty_dict,
-    empty_list,
-)
+from linkml_runtime.utils.metamodelcore import Bool, XSDDate, empty_dict, empty_list
 from linkml_runtime.utils.slot import Slot
-from linkml_runtime.utils.yamlutils import (
-    YAMLRoot,
-    extended_str,
-)
+from linkml_runtime.utils.yamlutils import YAMLRoot, extended_str
 from rdflib import URIRef
 
 metamodel_version = "1.7.0"