Merge pull request #229 from ga4gh/range_serialization

Minor changes to how direct and indirect ranges are serialized

src/ga4gh/core/_internal/identifiers.py

@@ -28,7 +28,7 @@
     is_identifiable,
     getattr_in,
     get_pydantic_root,
-    is_pydantic_custom_str_type
+    is_pydantic_custom_type
 )
 
 __all__ = "ga4gh_digest ga4gh_identify ga4gh_serialize is_ga4gh_identifier parse_ga4gh_identifier".split()
@@ -197,9 +197,9 @@ def identify_all(
     if input_obj is None:
         return None
     output_obj = input_obj
-    if is_pydantic_custom_str_type(input_obj):
+    if is_pydantic_custom_type(input_obj):
         val = export_pydantic_model(input_obj)
-        if is_curie_type(val) and is_ga4gh_identifier(val):
+        if isinstance(val, str) and is_curie_type(val) and is_ga4gh_identifier(val):
             val = parse_ga4gh_identifier(val)["digest"]
         output_obj = val
     elif is_pydantic_instance(input_obj):

src/ga4gh/core/_internal/pydantic.py

@@ -64,6 +64,9 @@ def get_pydantic_root(obj: Union[Any, RootModel]) -> Any:
     return obj
 
 
+def is_pydantic_custom_type(obj: RootModel) -> bool:
+    return isinstance(obj, RootModel)
+
 def is_pydantic_custom_str_type(obj: RootModel) -> bool:
     return isinstance(obj, RootModel) and isinstance(obj.root, str)
 

src/ga4gh/vrs/_internal/models.py

@@ -243,6 +243,7 @@ class IRI(RootModel):
 class SequenceReference(BaseModel):
     model_config = ConfigDict(
         extra='allow',
+        use_enum_values=True
     )
     id: Optional[str] = Field(
         None,
@@ -295,7 +296,6 @@ class ReferenceLengthExpression(BaseModel):
 
 
 
-
 class LiteralSequenceExpression(BaseModel):
     model_config = ConfigDict(
         extra='allow',
@@ -315,6 +315,7 @@ class LiteralSequenceExpression(BaseModel):
 class Mapping(BaseModel):
     model_config = ConfigDict(
         extra='allow',
+        use_enum_values=True
     )
     id: Optional[str] = Field(
         None,
@@ -481,6 +482,7 @@ class ga4gh:
 class CopyNumberChange(BaseModel):
     model_config = ConfigDict(
         extra='allow',
+        use_enum_values=True
     )
     id: Optional[str] = Field(
         None,

src/ga4gh/vrs/extras/variation_normalizer_rest_dp.py

@@ -16,15 +16,15 @@ def to_hgvs(self, vo, namespace="refseq"):
         Use this method if you don't have UTA installed locally or are unable
         to reach the public UTA database due to port issues.
         """
-        vo = vo.model_dump()
+        vo = vo.model_dump(exclude_none=True)
         data = dict(
-            variation = vo,
-            namespace = namespace
+            variation=vo,
+            namespace=namespace
         )
         r = requests.post(
-            url = f"{self.api}/vrs_allele_to_hgvs",
+            url=f"{self.api}/vrs_allele_to_hgvs",
             json=data,
-            headers={ "Content-Type": "application/json; charset=utf-8" }
+            headers={"Content-Type": "application/json; charset=utf-8"}
         )
         if r.status_code == 200:
             return r.json().get("variations", [])

src/ga4gh/vrs/normalize.py

@@ -18,15 +18,12 @@
 def _normalize_allele(allele, data_proxy):
     sequence = SequenceProxy(data_proxy, allele.location.sequence)
 
-    ival = (allele.location.start.value, allele.location.end)
+    ival = (allele.location.start, allele.location.end)
 
     _allele_state = allele.state.type
-    _states_with_sequence = ["SequenceState", "LiteralSequenceExpression"]
+    _states_with_sequence = ["ReferenceLengthExpression", "LiteralSequenceExpression"]
     if _allele_state in _states_with_sequence:
         alleles = (None, allele.state.sequence)
-    elif _allele_state == "RepeatedSequenceExpression" and \
-            allele.state.seq_expr.type in _states_with_sequence:
-        alleles = (None, allele.state.seq_expr.sequence)
     else:
         alleles = (None, "")
 

tests/validation/test_models.py

@@ -42,6 +42,6 @@ def flatten_tests(vts):
 
 @pytest.mark.parametrize("cls,data,fn,exp", flatten_tests(validation_tests))
 def test_validation(cls, data, fn, exp):
-    o = models[cls](**data)
+    o = getattr(models, cls)(**data)
     fx = fxs[fn]
     assert exp == fx(o)