Trapi 2.0.0-beta2 compliance (and fixes)

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "uv_build"
 
 [project]
 name = "translator_tom"
-version = "2.0.0"
+version = "2.1.0"
 description = "TRAPI Object Models: A performant python data model and centralized utilities for the Translator Reasoner API."
 readme = "README.md"
 requires-python = ">=3.10"

src/translator_tom/v1_6/model_dicts/workflow_operations.py

@@ -61,8 +61,8 @@
     OverlayComputeNgdParameters,
     OverlayFisherExactTestParameters,
     PlusOrMinus,
-    SortResultNodeAttributeParameters,
     SortResultsEdgeAttributeParameters,
+    SortResultsNodeAttributeParameters,
     SortResultsScoreParameters,
     TopOrBottom,
 )
@@ -169,10 +169,10 @@
     "OverlayFisherExactTestParametersDict",
     "OverlayFisherExactTestParametersDictUtil",
     "RunnerParametersDict",
-    "SortResultNodeAttributeParametersDict",
-    "SortResultNodeAttributeParametersDictUtil",
     "SortResultsEdgeAttributeParametersDict",
     "SortResultsEdgeAttributeParametersDictUtil",
+    "SortResultsNodeAttributeParametersDict",
+    "SortResultsNodeAttributeParametersDictUtil",
     "SortResultsScoreParametersDict",
     "SortResultsScoreParametersDictUtil",
 ]
@@ -783,22 +783,22 @@ class OperationSortResultsEdgeAttributeDictUtil(BaseOperationDictUtil):
     _model = OperationSortResultsEdgeAttribute
 
 
-class SortResultNodeAttributeParametersDict(OperationParametersDict):
+class SortResultsNodeAttributeParametersDict(OperationParametersDict):
     node_attribute: str
     ascending_or_descending: AscendingOrDescending
-    qnode_keys: list[QNodeID] | None
+    qnode_keys: NotRequired[list[QNodeID] | None]
 
 
-class SortResultNodeAttributeParametersDictUtil(
-    DictUtil[SortResultNodeAttributeParametersDict]
+class SortResultsNodeAttributeParametersDictUtil(
+    DictUtil[SortResultsNodeAttributeParametersDict]
 ):
-    """Utility methods for `SortResultNodeAttributeParametersDict`, mirroring the model."""
+    """Utility methods for `SortResultsNodeAttributeParametersDict`, mirroring the model."""
 
-    _model = SortResultNodeAttributeParameters
+    _model = SortResultsNodeAttributeParameters
 
     @staticmethod
     def qnode_keys_list(
-        parameters: SortResultNodeAttributeParametersDict,
+        parameters: SortResultsNodeAttributeParametersDict,
     ) -> list[QNodeID]:
         """Return a guaranteed list of qnode_keys, empty if it is not defined."""
         qnode_keys = parameters.get("qnode_keys")
@@ -807,7 +807,7 @@ def qnode_keys_list(
 
 class OperationSortResultsNodeAttributeDict(BaseOperationDict):
     id: Literal["sort_results_node_attribute"]
-    parameters: SortResultNodeAttributeParametersDict
+    parameters: SortResultsNodeAttributeParametersDict
 
 
 class OperationSortResultsNodeAttributeDictUtil(BaseOperationDictUtil):

src/translator_tom/v1_6/models/workflow_operations.py

@@ -68,8 +68,8 @@
     "PlusOrMinus",
     "PlusOrMinusEnum",
     "RunnerParameters",
-    "SortResultNodeAttributeParameters",
     "SortResultsEdgeAttributeParameters",
+    "SortResultsNodeAttributeParameters",
     "SortResultsScoreParameters",
     "TopOrBottom",
     "TopOrBottomEnum",
@@ -714,15 +714,15 @@ class OperationSortResultsEdgeAttribute(BaseOperation):
     parameters: SortResultsEdgeAttributeParameters
 
 
-class SortResultNodeAttributeParameters(OperationParameters):
-    """Parameters for the SortResultNodeAttribute operation."""
+class SortResultsNodeAttributeParameters(OperationParameters):
+    """Parameters for the SortResultsNodeAttribute operation."""
 
     node_attribute: Annotated[str, Field(examples=["normalized_google_distance"])]
     """The name of the node attribute to order by."""
 
     ascending_or_descending: AscendingOrDescending
 
-    qnode_keys: Annotated[list[QNodeID] | None, Field(examples=["[e01]"])]
+    qnode_keys: Annotated[list[QNodeID] | None, Field(examples=["[e01]"])] = None
     """This indicates if you only want to consider nodes with specific node_keys.
 
     If not provided or empty, all nodes will be looked at.
@@ -744,7 +744,7 @@ class OperationSortResultsNodeAttribute(BaseOperation):
     """
 
     id: Literal["sort_results_node_attribute"]
-    parameters: SortResultNodeAttributeParameters
+    parameters: SortResultsNodeAttributeParameters
 
 
 class SortResultsScoreParameters(OperationParameters):

src/translator_tom/v1_6/validation/_workflow_operations.py

@@ -27,8 +27,8 @@
     OverlayComputeJaccardParameters,
     OverlayComputeNgdParameters,
     OverlayFisherExactTestParameters,
-    SortResultNodeAttributeParameters,
     SortResultsEdgeAttributeParameters,
+    SortResultsNodeAttributeParameters,
 )
 from translator_tom.v1_6.validation._util import (
     Location,
@@ -300,9 +300,9 @@ def _validate_sort_edge_attr_params(
     )
 
 
-@semantic_validate.register(SortResultNodeAttributeParameters)
+@semantic_validate.register(SortResultsNodeAttributeParameters)
 def _validate_sort_node_attr_params(
-    obj: SortResultNodeAttributeParameters,
+    obj: SortResultsNodeAttributeParameters,
     location: Location | None = None,
     *,
     qgraph: QueryGraph | PathfinderQueryGraph | None = None,

src/translator_tom/v2_0/model_dicts/analysis.py

@@ -26,12 +26,12 @@
 
 class AnalysisDict(TypedDict):
     resource_id: CURIE
-    edge_bindings: NotRequired[dict[QEdgeID, EdgeBindingDict] | None]
-    path_bindings: NotRequired[dict[QPathID, PathBindingDict] | None]
-    score: NotRequired[float | None]
-    support_graphs: NotRequired[list[AuxGraphID] | None]
-    scoring_method: NotRequired[str | None]
-    attributes: NotRequired[list[AttributeDict] | None]
+    edge_bindings: NotRequired[dict[QEdgeID, EdgeBindingDict]]
+    path_bindings: NotRequired[dict[QPathID, PathBindingDict]]
+    score: NotRequired[float]
+    support_graphs: NotRequired[list[AuxGraphID]]
+    scoring_method: NotRequired[str]
+    attributes: NotRequired[list[AttributeDict]]
 
 
 class AnalysisDictUtil(DictUtil[AnalysisDict]):

src/translator_tom/v2_0/model_dicts/asyncquery.py

@@ -35,16 +35,16 @@ class AsyncQueryDict(QueryDict):
 
 
 class AsyncQueryResponseDict(TypedDict):
-    status: NotRequired[str | None]
-    description: NotRequired[str | None]
+    status: NotRequired[str]
+    description: NotRequired[str]
     job_id: str
 
 
 class AsyncQueryStatusResponseDict(TypedDict):
     status: str
     description: str
     logs: list[LogEntryDict]
-    response_url: NotRequired[str | None]
+    response_url: NotRequired[str]
 
 
 class AsyncQueryDictUtil(DictUtil[AsyncQueryDict]):

src/translator_tom/v2_0/model_dicts/attribute.py

@@ -28,13 +28,13 @@
 
 class AttributeDict(TypedDict):
     attribute_type_id: CURIE
-    original_attribute_name: NotRequired[str | None]
+    original_attribute_name: NotRequired[str]
     value: FastJsonValue
-    value_type_id: NotRequired[CURIE | None]
-    attribute_source: NotRequired[str | None]
-    value_url: NotRequired[str | None]
-    description: NotRequired[str | None]
-    attributes: NotRequired[list[AttributeDict] | None]
+    value_type_id: NotRequired[CURIE]
+    attribute_source: NotRequired[str]
+    value_url: NotRequired[str]
+    description: NotRequired[str]
+    attributes: NotRequired[list[AttributeDict]]
 
 
 class AttributeDictUtil(DictUtil[AttributeDict]):
@@ -82,12 +82,12 @@ def merge_attribute_lists(
     "AttributeConstraintDict",
     {
         "id": CURIE,
-        "name": NotRequired[str | None],
+        "name": NotRequired[str],
         "not": NotRequired[bool],
         "operator": Operator,
         "value": FastJsonValue,
-        "unit_id": NotRequired[CURIE | None],
-        "unit_name": NotRequired[str | None],
+        "unit_id": NotRequired[CURIE],
+        "unit_name": NotRequired[str],
     },
 )
 

src/translator_tom/v2_0/model_dicts/constraints.py

@@ -120,11 +120,11 @@ def met_by(
 
 
 class QEdgeConstraintsDict(TypedDict):
-    knowledge_level: NotRequired[KnowledgeLevelConstraintDict | None]
-    agent_type: NotRequired[AgentTypeConstraintDict | None]
-    attributes: NotRequired[list[AttributeConstraintDict] | None]
-    qualifiers: NotRequired[list[QualifierSetConstraint] | None]
-    sources: NotRequired[SourceConstraintDict | None]
+    knowledge_level: NotRequired[KnowledgeLevelConstraintDict]
+    agent_type: NotRequired[AgentTypeConstraintDict]
+    attributes: NotRequired[list[AttributeConstraintDict]]
+    qualifiers: NotRequired[list[QualifierSetConstraint]]
+    sources: NotRequired[SourceConstraintDict]
 
 
 class QEdgeConstraintsDictUtil(DictUtil[QEdgeConstraintsDict]):

src/translator_tom/v2_0/model_dicts/knowledge_graph.py

@@ -52,10 +52,10 @@
 
 
 class NodeDict(TypedDict):
-    name: NotRequired[str | None]
+    name: NotRequired[str]
     categories: list[Biolink.Entity]
-    attributes: NotRequired[list[AttributeDict] | None]
-    is_set: NotRequired[bool | None]
+    attributes: NotRequired[list[AttributeDict]]
+    is_set: NotRequired[bool]
 
 
 class NodeDictUtil(DictUtil[NodeDict]):
@@ -90,7 +90,9 @@ def update(node: NodeDict, other: NodeDict) -> None:
 
         Does not mutate `other`.
         """
-        node["name"] = other.get("name") or node.get("name")
+        name = other.get("name") or node.get("name")
+        if name is not None:
+            node["name"] = name
         node["categories"] = list(set(node["categories"]) | set(other["categories"]))
 
         other_attrs = other.get("attributes")
@@ -108,8 +110,8 @@ class EdgeDict(TypedDict):
     predicate: Biolink.Predicate
     subject: CURIE
     object: CURIE
-    attributes: NotRequired[list[AttributeDict] | None]
-    qualifiers: NotRequired[list[QualifierDict] | None]
+    attributes: NotRequired[list[AttributeDict]]
+    qualifiers: NotRequired[list[QualifierDict]]
     sources: list[RetrievalSourceDict]
     knowledge_level: str
     agent_type: str
@@ -313,7 +315,7 @@ def append_aggregator(edge: EdgeDict, source: Infores) -> None:
 
 class KnowledgeGraphDict(TypedDict):
     nodes: dict[CURIE, NodeDict]
-    edges: NotRequired[dict[EdgeID, EdgeDict] | None]
+    edges: NotRequired[dict[EdgeID, EdgeDict]]
 
 
 class KnowledgeGraphDictUtil(DictUtil[KnowledgeGraphDict]):
@@ -490,9 +492,11 @@ def prune(
             for aux_graph_id in cast("list[str]", edge_aux_graphs["value"]):
                 edges_to_check.extend(aux_graphs[aux_graph_id]["edges"])
 
-        knowledge_graph["edges"] = {
-            edge_id: edges[edge_id] for edge_id in bound_edges
-        } or None
+        bound = {edge_id: edges[edge_id] for edge_id in bound_edges}
+        if bound:
+            knowledge_graph["edges"] = bound
+        else:
+            knowledge_graph.pop("edges", None)
         knowledge_graph["nodes"] = {
             curie: knowledge_graph["nodes"][curie] for curie in bound_nodes
         }

src/translator_tom/v2_0/model_dicts/log_entry.py

@@ -12,8 +12,8 @@
 
 class LogEntryDict(TypedDict):
     timestamp: str
-    level: NotRequired[LogLevel | None]
-    code: NotRequired[str | None]
+    level: NotRequired[LogLevel]
+    code: NotRequired[str]
     message: str
 
 

src/translator_tom/v2_0/model_dicts/message.py

@@ -27,10 +27,10 @@
 
 
 class MessageDict(TypedDict):
-    results: NotRequired[list[ResultDict] | None]
-    query_graph: NotRequired[QueryGraphDict | None]
-    knowledge_graph: NotRequired[KnowledgeGraphDict | None]
-    auxiliary_graphs: NotRequired[dict[AuxGraphID, AuxiliaryGraphDict] | None]
+    results: NotRequired[list[ResultDict]]
+    query_graph: NotRequired[QueryGraphDict]
+    knowledge_graph: NotRequired[KnowledgeGraphDict]
+    auxiliary_graphs: NotRequired[dict[AuxGraphID, AuxiliaryGraphDict]]
 
 
 def _query_graph_hash(query_graph: QueryGraphDict | None) -> str | None:

src/translator_tom/v2_0/model_dicts/meta_attribute.py

@@ -12,10 +12,10 @@
 
 class MetaAttributeDict(TypedDict):
     attribute_type_id: CURIE
-    attribute_source: NotRequired[str | None]
-    original_attribute_names: NotRequired[list[str] | None]
+    attribute_source: NotRequired[str]
+    original_attribute_names: NotRequired[list[str]]
     constraint_use: NotRequired[bool]
-    constraint_name: NotRequired[str | None]
+    constraint_name: NotRequired[str]
 
 
 class MetaAttributeDictUtil(DictUtil[MetaAttributeDict]):