Merge pull request #667 from kids-first/remove-delete-sample-orphan

♻️ Don't delete samples with 0 biospecimens

dataservice/api/sample/models.py

@@ -30,13 +30,9 @@
 
 class Sample(db.Model, Base):
     """
-    Sample - a biologically equivalent group of specimens
+    Sample - a biologically distinct unit
 
-    Background:
-
-    The current Biospecimen table does not adequately model the hierarchical
-    relationship between specimen groups and specimens. The Sample table has
-    been created to fill in this gap.
+    The Biospecimen represents an aliquot or portion of a Sample
 
     :param kf_id: Unique id given by the Kid's First DCC
     :param external_id: Name given to sample by contributor
@@ -108,13 +104,3 @@ class Sample(db.Model, Base):
     biospecimens = db.relationship(
         Biospecimen, backref=db.backref('sample', lazy=True)
     )
-
-
-@event.listens_for(Biospecimen, 'after_delete')
-def delete_orphans(mapper, connection, state):
-    """
-    Delete samples with 0 child biospecimens
-    """
-    q = (db.session.query(Sample)
-         .filter(~Sample.biospecimens.any()))
-    q.delete(synchronize_session='fetch')

tests/sample/test_sample_models.py

@@ -38,9 +38,9 @@ def test_delete_sample(self):
 
         assert Biospecimen.query.get(bs_kf_id).sample_id is None
 
-    def test_delete_sample_orphan(self):
+    def test_no_delete_sample_orphan(self):
         """
-        Test that a sample is deleted when all related biospecimens
+        Test that a sample is NOT deleted when all related biospecimens
         are deleted
         """
         # Make two samples with biospecimens
@@ -60,13 +60,13 @@ def test_delete_sample_orphan(self):
             db.session.delete(ct)
         db.session.commit()
 
-        # Check that orphan sample is deleted
+        # Check that orphan sample is not deleted
         result = Sample.query.filter_by(external_id="s01").one_or_none()
-        assert result is None
+        assert result.kf_id
 
         # Check that other sample still exists
         result = Sample.query.filter_by(external_id="s02").one_or_none()
-        assert result
+        assert result.kf_id
         assert len(result.biospecimens) == 1
 
     def test_update_sample(self):