Only count sampled_portion for direct inputs

Author: naglepuff

nmdc_server/ingest/omics_processing.py

@@ -67,14 +67,23 @@ def find_parent_process(output_id: str, mongodb: Database) -> Optional[dict[str,
 
 
 def get_biosample_input_ids(
-    input_id: str, mongodb: Database, results: set[str], sampled_portions: set[str]
+    input_id: str,
+    mongodb: Database,
+    results: set[str],
+    sampled_portions: set[str],
+    direct_input: bool,
 ) -> set[Any]:
     """
     Given an input ID return all biosample objects that are included in the input resource.
 
     OmicsProcessing objects can take Biosamples or ProcessedSamples as inputs. Work needs to be done
     to determine which biosamples make up a given ProcessedSample. This function recursively tries
     to determine those Biosamples.
+
+    As a side effect, a set of `sampled_portion` values gets populated. Whether or not a processed
+    samples' `sampled_portion`s get added to the set is driven by the `direct_input` parameter. Only
+    processed samples who are inputs directly to a data generation will have their
+    `sampled_portion`s added.
     """
     # Base case, the input is already a biosample
     biosample_collection: Collection = mongodb["biosample_set"]
@@ -92,15 +101,16 @@ def get_biosample_input_ids(
     processed_sample = query[0]
     processed_sample_id = processed_sample["id"]
     sampled_portion = set(processed_sample.get("sampled_portion", []))
-    if sampled_portion:
+    # only store sampled portion values for immediate input to a data generation
+    if direct_input and sampled_portion:
         sampled_portions.update(sampled_portion)
 
     # Recursive case. For processed samples find the process that created it,
     # and check the inputs of that process.
     parent_process = find_parent_process(processed_sample_id, mongodb)
     if parent_process:
         for parent_input_id in parent_process["has_input"]:
-            get_biosample_input_ids(parent_input_id, mongodb, results, sampled_portions)
+            get_biosample_input_ids(parent_input_id, mongodb, results, sampled_portions, False)
     return results
 
 
@@ -145,7 +155,7 @@ def load_omics_processing(db: Session, obj: Dict[str, Any], mongodb: Database, l
     sampled_portions: set[str] = set()
     for input_id in input_ids:
         biosample_input_ids.union(
-            get_biosample_input_ids(input_id, mongodb, biosample_input_ids, sampled_portions)
+            get_biosample_input_ids(input_id, mongodb, biosample_input_ids, sampled_portions, True)
         )
     if sampled_portions:
         obj["sampled_portions"] = list(sampled_portions)