Merge pull request #1 from ialarmedalien/test_transformer_examples_tidy

Flesh out transformation tests

tests/input/examples/measurements/data/PersonQuantityValue-002.yaml

@@ -0,0 +1,4 @@
+id: P:2
+height:
+  value: 1.72
+  unit: m

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

@@ -7,6 +7,8 @@ persons:
     has_familial_relationships:
       - type: SIBLING_OF
         related_to: P:002
+      - type: CHILD_OF
+        related_to: P:003
     current_address:
       street: 1 oak street
     aliases:
@@ -23,10 +25,19 @@ persons:
     has_familial_relationships:
       - type: SIBLING_OF
         related_to: P:001
+      - type: CHILD_OF
+        related_to: P:003
     has_medical_history:
       - diagnosis:
           id: C:001
           name: c1 (renamed)
+  - id: P:003
+    name: Mr. Blobby
+    has_familial_relationships:
+      - type: PARENT_OF
+        related_to: P:001
+      - type: PARENT_OF
+        related_to: P:002
 organizations:
   - id: ROR:1
-    name: Acme
+    name: Acme

tests/input/examples/personinfo_basic/data/Person-001.yaml

@@ -6,6 +6,8 @@ gender: nonbinary man
 has_familial_relationships:
   - type: SIBLING_OF
     related_to: P:002
+  - type: CHILD_OF
+    related_to: P:003
 current_address:
   street: 1 oak street
-  city: oaktown
+  city: oaktown

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

@@ -1,32 +1,40 @@
-# Auto generated from personinfo_s2.yaml by pythongen.py version: 0.9.0
-# Generation date: 2023-02-04T18:11:52
+# Auto generated from agent.yaml by pythongen.py version: 0.9.0
+# Generation date: 2023-04-14T14:30:22
 # Schema: personinfo
 #
 # id: https://w3id.org/linkml/examples/personinfo
 # description: Information about people, based on [schema.org](http://schema.org)
 # license: https://creativecommons.org/publicdomain/zero/1.0/
 
 import dataclasses
-import re
 import sys
+import re
+from jsonasobj2 import JsonObj, as_dict
+from typing import Optional, List, Union, Dict, ClassVar, Any
 from dataclasses import dataclass
-from typing import Any, ClassVar, Dict, List, Optional, Union
+from linkml_runtime.linkml_model.meta import (
+    EnumDefinition,
+    PermissibleValue,
+    PvFormulaOptions,
+)
 
-from jsonasobj2 import JsonObj, as_dict
-from linkml_runtime.linkml_model.meta import (EnumDefinition, PermissibleValue,
-                                              PvFormulaOptions)
-from linkml_runtime.linkml_model.types import Boolean, Date, Float, String
-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.formatutils import camelcase, sfx, underscore
-from linkml_runtime.utils.metamodelcore import (Bool, XSDDate, bnode,
-                                                empty_dict, empty_list)
 from linkml_runtime.utils.slot import Slot
-from linkml_runtime.utils.yamlutils import (YAMLRoot, extended_float,
-                                            extended_int, extended_str)
+from linkml_runtime.utils.metamodelcore import empty_list, empty_dict, bnode
+from linkml_runtime.utils.yamlutils import (
+    YAMLRoot,
+    extended_str,
+    extended_float,
+    extended_int,
+)
+from linkml_runtime.utils.dataclass_extensions_376 import (
+    dataclasses_init_fn_with_kwargs,
+)
+from linkml_runtime.utils.formatutils import camelcase, underscore, sfx
+from linkml_runtime.utils.enumerations import EnumDefinitionImpl
 from rdflib import Namespace, URIRef
+from linkml_runtime.utils.curienamespace import CurieNamespace
+from linkml_runtime.linkml_model.types import Boolean, Date, Float, String
+from linkml_runtime.utils.metamodelcore import Bool, XSDDate
 
 metamodel_version = "1.7.0"
 version = None
@@ -153,6 +161,7 @@ class Agent(NamedThing):
     has_medical_history: Optional[
         Union[Union[dict, "MedicalEvent"], List[Union[dict, "MedicalEvent"]]]
     ] = empty_list()
+    parents: Optional[Union[str, List[str]]] = empty_list()
     aliases: Optional[Union[str, List[str]]] = empty_list()
 
     def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
@@ -213,6 +222,10 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
             for v in self.has_medical_history
         ]
 
+        if not isinstance(self.parents, list):
+            self.parents = [self.parents] if self.parents is not None else []
+        self.parents = [v if isinstance(v, str) else str(v) for v in self.parents]
+
         if not isinstance(self.aliases, list):
             self.aliases = [self.aliases] if self.aliases is not None else []
         self.aliases = [v if isinstance(v, str) else str(v) for v in self.aliases]
@@ -603,6 +616,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
 # Enumerations
 class FamilialRelationshipType(EnumDefinitionImpl):
     SIBLING_OF = PermissibleValue(text="SIBLING_OF", meaning=FAMREL["01"])
+    CHILD_OF = PermissibleValue(text="CHILD_OF", meaning=FAMREL["05"])
 
     _defn = EnumDefinition(
         name="FamilialRelationshipType",
@@ -613,9 +627,6 @@ def _addvals(cls):
         setattr(
             cls, "parent of", PermissibleValue(text="parent of", meaning=FAMREL["02"])
         )
-        setattr(
-            cls, "child of", PermissibleValue(text="child of", meaning=FAMREL["01"])
-        )
 
 
 class GenderType(EnumDefinitionImpl):
@@ -782,6 +793,15 @@ class slots:
     ],
 )
 
+slots.parents = Slot(
+    uri=PERSONINFO.parents,
+    name="parents",
+    curie=PERSONINFO.curie("parents"),
+    model_uri=PERSONINFO.parents,
+    domain=None,
+    range=Optional[Union[str, List[str]]],
+)
+
 slots.in_location = Slot(
     uri=PERSONINFO.in_location,
     name="in_location",
@@ -970,15 +990,6 @@ class slots:
     range=Optional[Union[str, List[str]]],
 )
 
-slots.related_to = Slot(
-    uri=PERSONINFO.related_to,
-    name="related to",
-    curie=PERSONINFO.curie("related_to"),
-    model_uri=PERSONINFO.related_to,
-    domain=None,
-    range=Union[str, AgentId],
-)
-
 slots.Agent_primary_email = Slot(
     uri=SCHEMA.email,
     name="Agent_primary_email",
@@ -1000,7 +1011,7 @@ class slots:
 
 slots.FamilialRelationship_related_to = Slot(
     uri=PERSONINFO.related_to,
-    name="FamilialRelationship_related to",
+    name="FamilialRelationship_related_to",
     curie=PERSONINFO.curie("related_to"),
     model_uri=PERSONINFO.FamilialRelationship_related_to,
     domain=FamilialRelationship,

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

@@ -613,7 +613,7 @@ class RelationshipType(EnumDefinitionImpl):
 class FamilialRelationshipType(EnumDefinitionImpl):
     SIBLING_OF = PermissibleValue(text="SIBLING_OF", meaning=FAMREL["01"])
     PARENT_OF = PermissibleValue(text="PARENT_OF", meaning=FAMREL["02"])
-    CHILD_OF = PermissibleValue(text="CHILD_OF", meaning=FAMREL["01"])
+    CHILD_OF = PermissibleValue(text="CHILD_OF", meaning=FAMREL["05"])
     FATHER_OF = PermissibleValue(text="FATHER_OF", meaning=FAMREL["11"])
 
     _defn = EnumDefinition(

tests/input/examples/personinfo_basic/source/personinfo.yaml

@@ -119,7 +119,6 @@ classes:
   ProcedureConcept:
     is_a: Concept
 
-
   Relationship:
     slots:
       - started_at_time
@@ -254,7 +253,7 @@ enums:
       PARENT_OF:
         meaning: famrel:02
       CHILD_OF:
-        meaning: famrel:01
+        meaning: famrel:05
       FATHER_OF:
         meaning: famrel:11
   GenderType:

tests/input/examples/personinfo_basic/target/agent.yaml

@@ -58,6 +58,7 @@ classes:
       - has_employment_history
       - has_familial_relationships
       - has_medical_history
+      - parents
     slot_usage:
       primary_email:
         pattern: "^\\S+@[\\S+\\.]+\\S+"
@@ -120,7 +121,6 @@ classes:
   ProcedureConcept:
     is_a: Concept
 
-
   Relationship:
     slots:
       - started_at_time
@@ -134,7 +134,7 @@ classes:
       type:
         range: FamilialRelationshipType
         required: true
-      related to:
+      related_to:
         range: Agent
         required: true
 
@@ -195,6 +195,10 @@ slots:
     range: FamilialRelationship
     multivalued: true
     inlined_as_list: true
+  parents:
+    range: string
+    multivalued: true
+    inlined_as_list: true
   in_location:
     range: Place
   current_address:
@@ -250,8 +254,8 @@ enums:
         meaning: famrel:01
       parent of:
         meaning: famrel:02
-      child of:
-        meaning: famrel:01
+      CHILD_OF:
+        meaning: famrel:05
   GenderType:
     permissible_values:
       nonbinary man:

tests/input/examples/personinfo_basic/transform/personinfo-to-agent.transform.yaml

@@ -18,7 +18,6 @@ class_derivations:
     is_a: Entity
     populated_from: Person
     slot_derivations:
-
       ## implicitly same name in Agent
       id:
 
@@ -42,21 +41,22 @@ class_derivations:
       ## unit conversion
       #age_in_years:
       #  expr: "units.convert(age.value, age.unit, units.YEARS)"
-        
+
       ## nested to flat
       #friends:
       #  expr: "[x.id for x in {friends}]"
 
       ## copy recursively, flat to nested
       #jobs:
       #  populated_from: jobs
-        
+
       ## copy recursively
       #diagnoses:
       #  populated_from: diagnoses
 
       has_familial_relationships:
         populated_from: has_familial_relationships
+
   Job:
     #primitive: uriorcurie
     slot_derivations:
@@ -94,7 +94,7 @@ class_derivations:
         type_designator: true
         hide: true
         populated_from: feature_type
-        
+
   DenormMapping:
     populated_from: Mapping
     #joins:
@@ -123,4 +123,6 @@ enum_derivations:
     populated_from: FamilialRelationshipType
     permissible_value_derivations:
       sibling of:
-        populated_from: SIBLING_OF
+        populated_from: SIBLING_OF
+      CHILD_OF:
+        populated_from: CHILD_OF