handle missing values and aggregation of a single run with scatters

omics/cli/run_analyzer/batch.py

@@ -104,16 +104,19 @@ def _do_aggregation(resources_list: list[dict], resource_key: str, operation: st
             # special case for instance types
             instances = []
             for r in resources_list:
-                instances.append(r["metrics"][resource_key])
+                if resource_key in r["metrics"]:
+                    instances.append(r["metrics"][resource_key])
             return max(instances, key=lambda x: utils.omics_instance_weight(x))
         else:
-            try:
-                return max([r["metrics"][resource_key] for r in resources_list])
-            except KeyError:
-                print(f"KeyError for {resource_key} in {resources_list}", file=sys.stderr)
+            return round(max([r["metrics"].get(resource_key, 0.0) for r in resources_list]), 4)
     elif operation == "mean":
-        return round(statistics.mean([r["metrics"][resource_key] for r in resources_list]), 2)
+        data = [r["metrics"].get(resource_key, 0.0) for r in resources_list]
+        return round(statistics.mean(data=data), 4)
     elif operation == "stdDev":
-        return round(statistics.stdev([r["metrics"][resource_key] for r in resources_list]), 2)
+        data = [r["metrics"].get(resource_key, 0.0) for r in resources_list]
+        if len(data) > 1:
+            return round(statistics.stdev(data=data), 4)
+        else:
+            return 0.000
     else:
         raise ValueError(f"Invalid aggregation operation: {operation}")

tests/cli/run_analyzer/unit/test_batch.py

@@ -80,7 +80,9 @@ def test_aggregate_and_print_resources(self):
             ],
         ]
         header_string = ",".join(batch.hdrs) + "\n"
-        expected = header_string + "task,foo,4,20.0,30.0,8.16,1.0,1.0,0,4,8,omics.c.large,1.0,1.0\n"
+        expected = (
+            header_string + "task,foo,4,20.0,30.0,8.165,1.0,1.0,0,4,8,omics.c.large,1.0,1.0\n"
+        )
         with io.StringIO() as result:
             batch.aggregate_and_print(
                 run_resources_list=resources_list, pricing={}, engine="WDL", out=result