test suite fixes

src/curate_gpt/agents/concept_recognition_agent.py

@@ -28,10 +28,10 @@ class Span(BaseModel):
     concept_id: str = None
     """Concept ID."""
 
-    concept_label: str = None
+    concept_label: Optional[str] = None
     """Concept label."""
 
-    is_suspect: bool = False
+    is_suspect: Optional[bool] = False
     """Potential hallucination due to ID/label mismatch."""
 
 

src/curate_gpt/cli.py

@@ -2442,6 +2442,7 @@ def view_objects(view, init_with, settings, object_ids, **kwargs):
     else:
         for obj in vstore.objects():
             print(yaml.dump(obj, sort_keys=False))
+            print("---")
 
 
 @view.command(name="unwrap")

src/curate_gpt/wrappers/clinical/maxoa_wrapper.py

@@ -96,6 +96,8 @@ def objects(
         # open a file handle from a URL using requests
         if source_locator is None:
             source_locator = self.source_locator
+        if source_locator is None:
+            source_locator = self.source_url
         if source_locator.startswith("http"):
             logger.info(f"Fetching {source_locator}")
             with requests.get(source_locator, stream=True) as response:

tests/agents/conftest.py

@@ -8,6 +8,12 @@
 
 @pytest.fixture
 def go_test_chroma_db() -> ChromaDBAdapter:
+    """
+    Fixture for a ChromaDBAdapter instance with the test ontology loaded.
+
+    Note: the chromadb is not checked into github - instead,
+    this relies on test_chromadb_dapter.test_store to create the test db.
+    """
     db = ChromaDBAdapter(str(INPUT_DBS / "go-nucleus-chroma"))
     db.schema_proxy = SchemaProxy(ONTOLOGY_MODEL_PATH)
     db.set_collection("test")

tests/agents/test_concept_recognizer.py

@@ -48,7 +48,7 @@ def test_concept_recognizer(go_test_chroma_db, text, categories, prefixes, expec
     cr.identifier_field = "original_id"
     print(f"## METHOD: {method} CATEGORY: {categories} PREFIXES: {prefixes}")
     ann = cr.annotate(
-        text, collection="terms_go", method=method, categories=categories, limit=limit
+        text, collection="test", method=method, categories=categories, limit=limit
     )
     print("RESULT:")
     print(yaml.dump(ann.dict(), sort_keys=False))