Second pass at type fixes

src/ontogpt/engines/knowledge_engine.py

@@ -80,7 +80,7 @@ class KnowledgeEngine(ABC):
     knowledge sources plus LLMs
     """
 
-    template: TEMPLATE_NAME = None
+    template: TEMPLATE_NAME = ""
     """LinkML Template to use for this engine.
     Must be of the form <module_name>.<ClassName>"""
 
@@ -92,40 +92,40 @@ class KnowledgeEngine(ABC):
     """Python class for the template.
     This is derived from the template and does not need to be set manually."""
 
-    template_module: ModuleType = None
+    template_module: ModuleType
     """Python module for the template.
     This is derived from the template and does not need to be set manually."""
 
     schemaview: SchemaView = None
     """LinkML SchemaView over the template.
     This is derived from the template and does not need to be set manually."""
 
-    api_key: str = None
+    api_key: str = ""
     """OpenAI API key."""
 
-    model: MODEL_NAME = None
+    model: MODEL_NAME = ""
     """Language Model. This may be overridden in subclasses."""
 
     # annotator: TextAnnotatorInterface = None
     # """Default annotator. TODO: deprecate?"""
 
-    annotators: Dict[str, List[TextAnnotatorInterface]] = None
+    annotators: Dict[str, List[TextAnnotatorInterface]]
     """Annotators for each class.
     An annotator will ground/map labels to CURIEs.
     These override the annotators annotated in the template
     """
 
-    skip_annotators: Optional[List[TextAnnotatorInterface]] = None
+    skip_annotators: Optional[List[TextAnnotatorInterface]]
     """Annotators to skip.
     This overrides any specified in the schema"""
 
-    mappers: List[BasicOntologyInterface] = None
+    mappers: List[BasicOntologyInterface]
     """List of concept mappers, to assist in grounding to desired ID prefix"""
 
-    labelers: List[BasicOntologyInterface] = None
+    labelers: List[BasicOntologyInterface]
     """Labelers that map CURIEs to labels"""
 
-    client: OpenAIClient = None
+    client: OpenAIClient
     """All calls to LLMs are delegated through this client"""
 
     dictionary: Dict[str, str] = field(default_factory=dict)
@@ -139,13 +139,13 @@ class KnowledgeEngine(ABC):
     named_entities: List[NamedEntity] = field(default_factory=list)
     """Cache of all named entities"""
 
-    auto_prefix: str = None
+    auto_prefix: str = ""
     """If set then non-normalized named entities will be mapped to this prefix"""
 
-    last_text: str = None
+    last_text: str = ""
     """Cache of last text."""
 
-    last_prompt: str = None
+    last_prompt: str = ""
     """Cache of last prompt used."""
 
     encoding = None
@@ -321,9 +321,10 @@ def promptable_slots(self, cls: Optional[ClassDefinition] = None) -> List[SlotDe
         return [s for s in sv.class_induced_slots(cls.name) if not self.slot_is_skipped(s)]
 
     def slot_is_skipped(self, slot: SlotDefinition) -> bool:
-        sv = self.schemaview
         if ANNOTATION_KEY_PROMPT_SKIP in slot.annotations:
             return True
+        else:
+            return False
 
     def normalize_named_entity(self, text: str, range: ElementName) -> str:
         """
@@ -558,7 +559,7 @@ def groundings(self, text: str, cls: ClassDefinition) -> Iterator[str]:
     #    raise NotImplementedError
 
     def merge_resultsets(
-        self, resultset: List[ExtractionResult], unique_fields: List[str] = None
+        self, resultset: List[ExtractionResult], unique_fields: List[str] = [""]
     ) -> ExtractionResult:
         """
         Merge all resultsets into a single resultset.

src/ontogpt/engines/mapping_engine.py

@@ -57,22 +57,22 @@ class Confidence(str, Enum):
 class CategorizedMapping(BaseModel):
     subject: CURIE = None
     object: CURIE = None
-    completion: str = None
+    completion: str = ""
     predicate: Union[MappingPredicate, str] = None
     confidence: Union[Confidence, str] = None
-    similarities: List[str] = None
-    differences: List[str] = None
+    similarities: List[str] = [""]
+    differences: List[str] = [""]
 
 
 class MappingTask(BaseModel):
     subject: CURIE
     object: CURIE
-    subject_label: str = None
-    object_label: str = None
-    subject_source: str = None
-    object_source: str = None
-    subject_adapter: str = None
-    object_adapter: str = None
+    subject_label: str = ""
+    object_label: str = ""
+    subject_source: str = ""
+    object_source: str = ""
+    subject_adapter: str = ""
+    object_adapter: str = ""
     predicate: Union[str, MappingPredicate] = None
     difficulty: Confidence = None
     score: float = None
@@ -97,11 +97,11 @@ class Relationship(BaseModel):
 class Concept(BaseModel):
     id: CURIE
     label: str
-    definition: str = None
-    synonyms: List[str] = []
-    parents: List[str] = []
+    definition: str = ""
+    synonyms: List[str] = [""]
+    parents: List[str] = [""]
     relationships: List[Relationship] = []
-    categories: List[str] = []
+    categories: List[str] = [""]
 
 
 @dataclass
@@ -112,7 +112,7 @@ class MappingEngine(KnowledgeEngine):
     object_adapter: BasicOntologyInterface = None
 
     def categorize_mapping(
-        self, subject: CURIE, object: CURIE, template_path: str = None
+        self, subject: CURIE, object: CURIE, template_path: str = ""
     ) -> CategorizedMapping:
         if template_path is None:
             template_path = DEFAULT_MAPPING_EVAL_PROMPT

src/ontogpt/engines/spires_engine.py

@@ -371,7 +371,7 @@ def _raw_extract(
         return payload
 
     def get_completion_prompt(
-        self, cls: ClassDefinition = None, text: str = None, object: OBJECT = None
+        self, cls: ClassDefinition = None, text: str = "", object: OBJECT = None
     ) -> str:
         """Get the prompt for the given template."""
         if cls is None: