add log warning re: missing variants

Author: nebfield

pgscatalog.core/src/pgscatalog/core/cli/combine_cli.py

@@ -99,13 +99,16 @@ def run():
             writer.write(dumped_variants)
             n_finished += 1
         finally:
-            variant_log.append(
-                ScoreLog(
-                    header=scorefile.header,
-                    variants=normalised_score,
-                    compatible_effect_type=is_compatible,
-                )
+            log = ScoreLog(
+                header=scorefile.header,
+                variants=normalised_score,
+                compatible_effect_type=is_compatible,
             )
+            if log.variants_are_missing:
+                logger.warning(
+                    f"{log.variant_count_difference} fewer variants in output compared to original file"
+                )
+            variant_log.append(log)
 
     if n_finished == 0:
         raise ValueError(

pgscatalog.core/src/pgscatalog/core/lib/models.py

@@ -725,12 +725,15 @@ def sources(self) -> Optional[list[str]]:
             return None
 
     @property
-    def n_actual_variants(self) -> int:
+    def n_actual_variants(self) -> Optional[int]:
         # this distinction is useful if variants have been filtered out
-        return len(self.variants)
+        if self.variants is not None:
+            return len(self.variants)
+        else:
+            return None
 
     @cached_property
-    def variant_count_difference(self) -> int:
+    def variant_count_difference(self) -> Optional[int]:
         # grab directly from header
         header_variants = getattr(self.header, "variants_number", None)
         if header_variants is None:
@@ -741,7 +744,10 @@ def variant_count_difference(self) -> int:
             else:
                 header_variants = self.header.row_count
 
-        return abs(header_variants - self.n_actual_variants)
+        try:
+            return abs(header_variants - self.n_actual_variants)
+        except TypeError:
+            return None
 
     @property
     def variants_are_missing(self) -> bool: