✅ Update all unit tests to support Study entity

tests/aliquot/test_aliquot_models.py

@@ -2,6 +2,7 @@
 import uuid
 
 from dataservice.extensions import db
+from dataservice.api.study.models import Study
 from dataservice.api.participant.models import Participant
 from dataservice.api.sample.models import Sample
 from dataservice.api.aliquot.models import Aliquot
@@ -20,6 +21,9 @@ def create_participant_sample_aliquot(self):
         create a participant, sample, and aliquot save to db
         returns participant_id, sample_id, and aliquot_id
         """
+        # Create study
+        study = Study(external_id='phs001')
+
         dt = datetime.now()
         participant_id = "Test_Subject_0"
         sample_id = "Test_Sample_0"
@@ -45,7 +49,8 @@ def create_participant_sample_aliquot(self):
         sample_0 = Sample(**sample_data, aliquots=[aliquot_0])
         participant_0 = Participant(
             external_id=participant_id,
-            samples=[sample_0])
+            samples=[sample_0],
+            study=study)
         db.session.add(participant_0)
         db.session.commit()
         return participant_id, sample_id, aliquot_id
@@ -67,10 +72,13 @@ def test_create_aliquot(self):
         """
         Test creation of aliquot
         """
+        # Create study
+        study = Study(external_id='phs001')
+
         dt = datetime.now()
         participant_id = "Test_Subject_0"
         # creating participant
-        p = Participant(external_id=participant_id)
+        p = Participant(external_id=participant_id, study=study)
         db.session.add(p)
         db.session.commit()
 

tests/demographic/test_demographic_models.py

@@ -3,6 +3,7 @@
 
 from sqlalchemy.exc import IntegrityError
 
+from dataservice.api.study.models import Study
 from dataservice.api.participant.models import Participant
 from dataservice.api.demographic.models import Demographic
 from dataservice.extensions import db
@@ -18,10 +19,13 @@ def test_create(self):
         """
         Test create demographic
         """
+        study = Study(external_id='phs001')
+        db.session.add(study)
+        db.session.commit()
 
         # Create and save participant
         participant_id = 'Test subject 0'
-        p = Participant(external_id=participant_id)
+        p = Participant(external_id=participant_id, study_id=study.kf_id)
         db.session.add(p)
         db.session.commit()
 
@@ -200,26 +204,13 @@ def test_get_participant_demographic(self):
         """
         Test get demographic via the participant
         """
-        # Create demographic
-        data = {
-            'external_id': 'demo_1',
-            'race': 'asian'
-        }
-        d = Demographic(**data)
-
-        # Create and save participant
-        participant_id = 'Test subject 0'
-        p = Participant(external_id=participant_id, demographic=d)
-        db.session.add(p)
-        db.session.commit()
+        # Create and save demographic
+        participant_id, demo_id = self._create_save_demographic()
 
         p = Participant.query.filter_by(external_id=participant_id).\
             one_or_none()
 
-        p_demo = p.demographic
-
-        self.assertEqual(p_demo.external_id, d.external_id)
-        self.assertEqual(p_demo.race, d.race)
+        self.assertEqual(p.demographic.external_id, demo_id)
 
     def _create_save_demographic(self):
         """
@@ -229,6 +220,11 @@ def _create_save_demographic(self):
         Create a demographic and add it to participant as kwarg
         Save participant
         """
+        # Create study
+        study = Study(external_id='phs001')
+        db.session.add(study)
+        db.session.commit()
+
         # Create demographic
         demo_id = 'demo_1'
         data = {
@@ -241,7 +237,8 @@ def _create_save_demographic(self):
 
         # Create and save participant
         participant_id = 'Test subject 0'
-        p = Participant(external_id=participant_id, demographic=d)
+        p = Participant(external_id=participant_id, demographic=d,
+                        study_id=study.kf_id)
         db.session.add(p)
         db.session.commit()
 

tests/demographic/test_demographic_resources.py

@@ -1,12 +1,12 @@
 import json
 from flask import url_for
 from urllib.parse import urlparse
-from pprint import pprint
 
 from dataservice.extensions import db
 from dataservice.api.common import id_service
 from dataservice.api.demographic.models import Demographic
 from dataservice.api.participant.models import Participant
+from dataservice.api.study.models import Study
 from tests.utils import FlaskTestCase
 
 DEMOGRAPHICS_URL = 'api.demographics'
@@ -21,8 +21,12 @@ def test_post(self):
         """
         Test create a new demographic
         """
+        study = Study(external_id='phs001')
+        db.session.add(study)
+        db.session.commit()
+
         # Create a participant
-        p = Participant(external_id='Test subject 0')
+        p = Participant(external_id='Test subject 0', study_id=study.kf_id)
         db.session.add(p)
         db.session.commit()
 
@@ -339,6 +343,10 @@ def _create_save_to_db(self):
         Create a demographic and add it to participant as kwarg
         Save participant
         """
+        study = Study(external_id='phs001')
+        db.session.add(study)
+        db.session.commit()
+
         # Create demographic
         kwargs = {
             'external_id': 'd1',
@@ -350,7 +358,8 @@ def _create_save_to_db(self):
 
         # Create and save participant with demographic
         participant_id = 'Test subject 0'
-        p = Participant(external_id=participant_id, demographic=d)
+        p = Participant(external_id=participant_id, demographic=d,
+                        study_id=study.kf_id)
         db.session.add(p)
         db.session.commit()