fix mypy

fhir_query/cli.py

@@ -211,7 +211,7 @@ def dataframe(db_path: str, output_path: str, launch_dtale: bool, data_type: str
         # TODO - add more data types - including condition
         assert data_type in ["Specimen", "Patient"], f"Sorry {data_type} dataframe is not supported yet."
 
-        df = None
+        df: pd.DataFrame | None = None
         if data_type == "Specimen":
             df = pd.DataFrame(db.flattened_specimens())
         if data_type == "Patient":
@@ -222,11 +222,13 @@ def dataframe(db_path: str, output_path: str, launch_dtale: bool, data_type: str
             import dtale
 
             dtale.show(df, subprocess=False, open_browser=True, port=40000)
-        else:
+        elif df is not None:
             # export to csv
             file_name = output_path if output_path else f"{data_type}.csv"
             df.to_csv(file_name, index=False)
             click.secho(f"Saved {file_name}", file=sys.stderr)
+        else:
+            click.secho(f"No data found for {data_type}", file=sys.stderr)
 
     except Exception as e:
         logging.error(f"Error: {e}", exc_info=True)

fhir_query/dataframer.py

@@ -293,11 +293,13 @@ def values(self) -> dict:
             return {}
 
         # update the key if code information is available
+
         if self.resource.get("code", {}).get("text", None):
             source = self.resource["code"]["text"]
         else:
             source = self.resource["code"]["coding"][0].get("display", self.resource["code"]["coding"][0].get("code"))
-
+        if not source:
+            source = "NA"
         source = inflection.underscore(inflection.parameterize(source))
         return {source: value}