fix issues pointed by linter and tests

src/anamnesisai/config.py

@@ -2,6 +2,8 @@
 
 from __future__ import annotations
 
+# prompt template for getting the given FHIR resource from the given
+# conversation between m.d. and patient.
 PROMPT_TEMPLATE = """
 You are a FHIR Resource generating expert. Given a conversion
 between doctor and patient, first create a syntactically correct
@@ -24,15 +26,18 @@
 Conversation:
 
 ```
-{query}
+{context}
 ```
 """.strip()
 
+# prompt template for checking possible FHIR resources present in the given
+# conversation
 PROMPT_TEMPLATE_POSSIBLE_RESOURCES = """
-please read the following conversation between patient and md doctor:
+please read the conversation between patient and md doctor in the given
+context:
 
 ```
-{query}
+{context}
 ```
 
 In the conversation, `D:` means it is from the Doctor, and `P:` means

src/anamnesisai/openai.py

@@ -41,7 +41,8 @@ def check_possible_fhir_resources(
             output_max_length=10384,  # note: calc this number
             structured_output=FHIRResourceFoundModel,
         )
-        result = gen.generate(query=text, context=[])
+        # the query is already present in the prompt template
+        result = gen.generate(query="", context=[text])
     except Exception as e:
         logging.debug(str(e))
         return FHIRResourceFoundModel()
@@ -82,7 +83,8 @@ def extract_fhir(text: str, api_key: str) -> dict[str, Resource]:
                 output_max_length=10384,  # note: calc this number
                 structured_output=fhir_class,
             )
-            result = gen.generate(query=text, context=[])
+            # the query is already present in the prompt template
+            result = gen.generate(query="", context=[text])
         except Exception as e:
             logging.warning(str(e))
             continue