✅ Fix broken tests - use sample/container mgr to create them

tests/biospecimen/test_sample_container_management.py

@@ -11,7 +11,6 @@
 from dataservice.api.container.models import Container
 from dataservice.api.sample.models import Sample
 from dataservice.api.biospecimen.models import Biospecimen
-from dataservice.api.biospecimen.manager import manage_sample_containers
 
 from tests.create import make_participant, make_seq_center
 
@@ -207,7 +206,7 @@ def test_create_two_biospecimens_diff_container(client, upsert_biospecimen):
     assert len(s.containers) == 2
 
     # Check container was created properly
-    for i, c in enumerate(s.containers):
+    for i, _ in enumerate(s.containers):
         check_container(specimens[i], s)
 
 

tests/conftest.py

@@ -39,6 +39,8 @@
     Task,
     TaskGenomicFile
 )
+from dataservice.api.biospecimen.manager import manage_sample_containers
+
 from unittest.mock import MagicMock, patch
 from tests.mocks import MockIndexd
 pytest_plugins = ['tests.mocks']
@@ -163,7 +165,7 @@ def make_entities(client):
                          BiospecimenDiagnosis,
                          ReadGroupGenomicFile,
                          SequencingExperimentGenomicFile,
-                         Container}:
+                         Sample, Container}:
                 continue
             for i in range(ENTITY_TOTAL):
                 data = ENTITY_PARAMS['fields'][endpoint].copy()
@@ -256,18 +258,6 @@ def make_entities(client):
             _entities[BiospecimenDiagnosis].append(bd)
             db.session.add(bd)
 
-        # Containers
-        samples = _entities[Sample]
-        biospecimens = _entities[Biospecimen]
-        for i, (sample, biospecimen) in enumerate(
-            zip(samples, biospecimens)
-        ):
-            ct = Container(external_id=f"container-{i}")
-            ct.sample = sample
-            ct.biospecimen = biospecimen
-            _entities[Container].append(ct)
-            db.session.add(ct)
-
         # Add relations
         s0 = _entities[Study][0]
         f0 = _entities[Family][0]
@@ -288,7 +278,7 @@ def make_entities(client):
 
         # Biospecimen, Diagnosis, Phenotype, Outcome
         participant_ents = [
-            Biospecimen, Diagnosis, Phenotype, Outcome, Sample
+            Biospecimen, Diagnosis, Phenotype, Outcome
         ]
         for participant_ent in participant_ents:
             for ent in _entities[participant_ent]:
@@ -306,6 +296,13 @@ def make_entities(client):
 
         db.session.commit()
 
+    # Create sample and containers from Biospecimens
+    for b in _entities[Biospecimen]:
+        s = manage_sample_containers(b)
+        _entities[Sample].append(s)
+        for c in s.containers:
+            _entities[Container].append(c)
+
     return _entities
 
 

tests/test_api.py

@@ -138,6 +138,7 @@ def test_parent_links(self, client, entities, endpoint, parents):
                            'biospecimens']),
         ('/biospecimens', ['biospecimen_genomic_files',
                            'biospecimen_diagnoses']),
+        ('/samples', ['containers']),
         ('/genomic-files', ['task_genomic_files',
                             'biospecimen_genomic_files',
                             'read_group_genomic_files',
@@ -389,8 +390,8 @@ def test_missing_required_params(self, client, entities, endpoint,
                               ('/study-files', 'study_id'),
                               ('/diagnoses', 'participant_id'),
                               ('/biospecimens', 'participant_id'),
-                              ('/containers', 'biospecimen_id'),
                               ('/samples', 'participant_id'),
+                              ('/containers', 'biospecimen_id'),
                               ('/tasks', 'cavatica_app_id'),
                               ('/task-genomic-files',
                                'task_id'),