more updates

src/ga4gh/core/models.py

@@ -90,7 +90,7 @@ class date(RootModel):
 
 class datetime(RootModel):
     """A string is valid against this format if it represents a date-time in the
-    following format: YYYY:MM::DDThh:mm:ss.sTZD..
+    following format: YYYY:MM::DDThh:mm:ss.sTZD.
     """
 
     root: datetime_datetime = Field(
@@ -212,7 +212,7 @@ class Extension(Element):
 
 
 class MappableConcept(Element):
-    """A concept label that may be mapped to one or more :ref:`Codings <Coding>`."""
+    """A concept label that may be mapped to one or more `Codings`."""
 
     conceptType: Optional[str] = Field(
         None,
@@ -232,7 +232,7 @@ class MappableConcept(Element):
     def require_label_or_primary_code(cls, v):
         """Ensure that ``label`` or ``primaryCode`` is provided"""
         if v.primaryCode is None and v.label is None:
-            err_msg = "`label` or `primaryCode` must be provided."
+            err_msg = "`One of label` or `primaryCode` must be provided."
             raise ValueError(err_msg)
         return v
 

src/ga4gh/vrs/models.py

@@ -703,12 +703,16 @@ class Adjacency(_VariationBase):
     homology: Optional[bool] = Field(None, description="A flag indicating if coordinate ambiguity in the adjoined sequences is from sequence homology (true) or other uncertainty, such as instrument ambiguity (false).")
 
     @field_validator("adjoinedSequences", mode="after")
-    def validate_adjoined_sequences(cls, v):
-        """Ensure ``adjoinedSequences`` does not have both ``start`` and ``end``"""
-        if isinstance(v, SequenceLocation):
-            if v.start and v.end:
-                err_msg = "Must not have both `start` and `end`."
-                raise err_msg
+    def validate_adjoined_sequences(cls, v) -> List[Union[iriReference, SequenceLocation]]:
+        """Ensure ``adjoinedSequences`` do not have both ``start`` and ``end``
+
+        :raises ValueError: If an adjoined sequence has both ``start`` and ``end``
+        """
+        for adjoined_seq in v:
+            if isinstance(adjoined_seq, SequenceLocation):
+                if adjoined_seq.start and adjoined_seq.end:
+                    err_msg = "Adjoined sequence must not have both `start` and `end`."
+                    raise ValueError(err_msg)
         return v
 
 
@@ -830,6 +834,25 @@ class CopyNumberChange(_VariationBase):
         description='MUST use a `primaryCode` representing one of "EFO:0030069" (complete genomic loss), "EFO:0020073" (high-level loss), "EFO:0030068" (low-level loss), "EFO:0030067" (loss), "EFO:0030064" (regional base ploidy), "EFO:0030070" (gain), "EFO:0030071" (low-level gain), "EFO:0030072" (high-level gain).',
     )
 
+    @field_validator("copyChange", mode="after")
+    def validate_copy_change(cls, v) -> MappableConcept:
+        """Validate that copyChange.primaryCode is an EFO code
+
+        :raises ValueError: If `primaryCode` is not provided or if its not a valid
+            EFO code
+        """
+        if v.primaryCode is None:
+            err_msg = "`primaryCode` is required."
+            raise ValueError(err_msg)
+
+        try:
+            CopyChange(v.primaryCode.root)
+        except ValueError:
+            err_msg = f"`primaryCode` must be one of: {[v.value for v in CopyChange.__members__.values()]}."
+            raise ValueError(err_msg)
+
+        return v
+
     class ga4gh(_Ga4ghIdentifiableObject.ga4gh):
         prefix = 'CX'
         keys = [

tests/validation/test_models.py

@@ -117,3 +117,27 @@ def test_valid_types():
                 assert not found_type_mismatch, f"Found mismatch in type literal: {enum_val} vs {error['ctx']['expected']}"
         else:
             assert False, f"{str(models)} class not found: {enum_val}"
+
+
+def test_mappable_concept():
+    """Test the MappableConcept model validator"""
+    # Does not provide required fields
+    with pytest.raises(ValueError, match="`One of label` or `primaryCode` must be provided."):
+        core_models.MappableConcept(conceptType="test")
+
+    # Valid models
+    assert core_models.MappableConcept(label="Primary Label")
+    assert core_models.MappableConcept(primaryCode="EFO:0030067")
+
+
+def test_copy_number_change():
+    """Test the CopyNumberChange field validator"""
+    location = core_models.iriReference("location.json#/1")
+
+    # Primary code not provided
+    with pytest.raises(ValueError, match="`primaryCode` is required."):
+        models.CopyNumberChange(location=location, copyChange=core_models.MappableConcept(label="test"))
+
+    # Primary code not valid EFO
+    with pytest.raises(ValueError, match="`primaryCode` must be one of:"):
+        models.CopyNumberChange(location=location, copyChange=core_models.MappableConcept(primaryCode="test"))