Merge pull request #695 from kids-first/ad-2303

✨ AD-2303 add amount and amount units to sample and bs and kf target
kids-first · Sep 10, 2024 · 159b4cc · 159b4cc
2 parents 2abcf8b + db88f80
commit 159b4cc
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Showing 2 changed files with 20 additions and 2 deletions.
diff --git a/kf_lib_data_ingest/common/concept_schema.py b/kf_lib_data_ingest/common/concept_schema.py
@@ -173,7 +173,11 @@ class SAMPLE(PropertyMixin):
         class EVENT_AGE(QuantityMixin):
             pass
 
+        class QUANTITY(QuantityMixin):
+            pass
+
         class VOLUME(QuantityMixin):
+            # Keeping for backwards compatability. Use QUANTITY instead.
             pass
 
         SPATIAL_DESCRIPTOR = None
@@ -186,8 +190,6 @@ class VOLUME(QuantityMixin):
         EXTERNAL_COLLECTION_ID = None
 
     class BIOSPECIMEN(SAMPLE):
-        class QUANTITY(QuantityMixin):
-            pass
 
         class CONCENTRATION(QuantityMixin):
             pass

diff --git a/kf_lib_data_ingest/target_api_plugins/kids_first_dataservice.py b/kf_lib_data_ingest/target_api_plugins/kids_first_dataservice.py
@@ -503,6 +503,14 @@ def build_entity(cls, record, get_target_id_from_record):
                 record.get(CONCEPT.SAMPLE.VOLUME_UL)
                 or record.get(CONCEPT.BIOSPECIMEN.VOLUME_UL)
             ),
+            "amount": (
+                record.get(CONCEPT.SAMPLE.QUANTITY.VALUE)
+                or record.get(CONCEPT.BIOSPECIMEN.QUANTITY.VALUE)
+            ),
+            "amount_units": (
+                record.get(CONCEPT.SAMPLE.QUANTITY.UNITS)
+                or record.get(CONCEPT.BIOSPECIMEN.QUANTITY.UNITS)
+            ),
         }
         return {
             **cls.get_key_components(record, get_target_id_from_record),
@@ -689,6 +697,14 @@ def build_entity(cls, record, get_target_id_from_record):
                 record.get(CONCEPT.SAMPLE.VOLUME_UL)
                 or record.get(CONCEPT.BIOSPECIMEN.VOLUME_UL)
             ),
+            "amount": (
+                record.get(CONCEPT.SAMPLE.QUANTITY.VALUE)
+                or record.get(CONCEPT.BIOSPECIMEN.QUANTITY.VALUE)
+            ),
+            "amount_units": (
+                record.get(CONCEPT.SAMPLE.QUANTITY.UNITS)
+                or record.get(CONCEPT.BIOSPECIMEN.QUANTITY.UNITS)
+            ),
             "specimen_status": (record.get(CONCEPT.BIOSPECIMEN.STATUS)),
             "visible": record.get(CONCEPT.BIOSPECIMEN.VISIBLE),
             "visibility_comment": record.get(