✅ Add tests for study resource

tests/conftest.py

@@ -101,6 +101,7 @@ def entities(client):
 
     # Add kf_ids
     inputs['kf_ids'] = {'/participants': p.kf_id}
+    inputs['kf_ids'].update({'/studies': study.kf_id})
     inputs['kf_ids'].update({'/demographics': p.demographic.kf_id})
     inputs['kf_ids'].update({'/diagnoses': diagnosis.kf_id})
     inputs['kf_ids'].update({'/samples': sample.kf_id})

tests/study/test_study_resources.py

@@ -0,0 +1,161 @@
+import json
+
+from flask import url_for
+
+from dataservice.extensions import db
+from dataservice.api.study.models import Study
+from tests.utils import FlaskTestCase
+
+STUDY_URL = 'api.studies'
+STUDY_LIST_URL = 'api.studies_list'
+
+
+class StudyTest(FlaskTestCase):
+    '''
+    Test study api endopoints
+    '''
+
+    def test_post_study(self):
+        '''
+        Test creating a new study
+        '''
+        response = self._make_study(external_id='TEST')
+        resp = json.loads(response.data.decode('utf-8'))
+
+        self.assertEqual(response.status_code, 201)
+        self._test_response_content(resp, 201)
+
+        self.assertIn('study', resp['_status']['message'])
+        self.assertIn('created', resp['_status']['message'])
+        self.assertNotIn('_id', resp['results'])
+
+        s = Study.query.first()
+        study = resp['results']
+        self.assertEqual(s.kf_id, study['kf_id'])
+        self.assertEqual(s.external_id, study['external_id'])
+
+    def test_get_study(self):
+        '''
+        Test retrieving a study by id
+        '''
+        resp = self._make_study('TEST')
+        resp = json.loads(resp.data.decode('utf-8'))
+        kf_id = resp['results']['kf_id']
+
+        response = self.client.get(url_for(STUDY_URL,
+                                           kf_id=kf_id),
+                                   headers=self._api_headers())
+        resp = json.loads(response.data.decode('utf-8'))
+        self.assertEqual(response.status_code, 200)
+        self._test_response_content(resp, 200)
+
+        study = resp['results']
+        self.assertEqual(kf_id, study['kf_id'])
+
+    def test_patch_study(self):
+        '''
+        Test updating an existing study
+        '''
+        response = self._make_study(external_id='TEST')
+        resp = json.loads(response.data.decode('utf-8'))
+        study = resp['results']
+        kf_id = study.get('kf_id')
+        external_id = study.get('external_id')
+
+        # Update the study via http api
+        body = {
+            'external_id': 'new_id'
+        }
+        response = self.client.patch(url_for(STUDY_URL,
+                                           kf_id=kf_id),
+                                   headers=self._api_headers(),
+                                   data=json.dumps(body))
+        self.assertEqual(response.status_code, 200)
+
+        self.assertEqual(Study.query.get(kf_id).external_id,
+                         body['external_id'])
+
+        resp = json.loads(response.data.decode('utf-8'))
+        self._test_response_content(resp, 200)
+        self.assertIn('study', resp['_status']['message'])
+        self.assertIn('updated', resp['_status']['message'])
+
+        study = resp['results']
+        self.assertEqual(study['kf_id'], kf_id)
+        self.assertEqual(study['external_id'], body['external_id'])
+
+    def test_patch_study_no_required_field(self):
+        '''
+        Test that we may update the study without a required field
+        '''
+        response = self._make_study(external_id='TEST')
+        resp = json.loads(response.data.decode('utf-8'))
+        study = resp['results']
+        kf_id = study.get('kf_id')
+        external_id = study.get('external_id')
+
+        # Update the study via http api
+        body = {
+            'version': '2.0'
+        }
+        response = self.client.patch(url_for(STUDY_URL,
+                                           kf_id=kf_id),
+                                   headers=self._api_headers(),
+                                   data=json.dumps(body))
+        self.assertEqual(response.status_code, 200)
+
+        self.assertEqual(Study.query.get(kf_id).version, '2.0')
+
+        resp = json.loads(response.data.decode('utf-8'))
+        self._test_response_content(resp, 200)
+        self.assertIn('study', resp['_status']['message'])
+        self.assertIn('updated', resp['_status']['message'])
+
+        study = resp['results']
+        self.assertEqual(study['kf_id'], kf_id)
+        self.assertEqual(study['external_id'], external_id)
+        self.assertEqual(study['version'], body['version'])
+
+    def test_delete_study(self):
+        '''
+        Test deleting a study by id
+        '''
+        resp = self._make_study('TEST')
+        resp = json.loads(resp.data.decode('utf-8'))
+        kf_id = resp['results']['kf_id']
+
+        response = self.client.delete(url_for(STUDY_URL,
+                                              kf_id=kf_id),
+                                      headers=self._api_headers())
+
+        resp = json.loads(response.data.decode('utf-8'))
+        self.assertEqual(response.status_code, 200)
+
+        response = self.client.get(url_for(STUDY_URL,
+                                           kf_id=kf_id),
+                                   headers=self._api_headers())
+
+        resp = json.loads(response.data.decode('utf-8'))
+        self.assertEqual(response.status_code, 404)
+
+    def _make_study(self, external_id='TEST-0001'):
+        '''
+        Convenience method to create a study with a given source name
+        '''
+        body = {
+            'external_id': external_id,
+            'version': '1.0'
+        }
+        response = self.client.post(url_for(STUDY_LIST_URL),
+                                    headers=self._api_headers(),
+                                    data=json.dumps(body))
+        return response
+
+    def _test_response_content(self, resp, status_code):
+        '''
+        Test that response body has expected fields
+        '''
+        self.assertIn('results', resp)
+        self.assertIn('_status', resp)
+        self.assertIn('message', resp['_status'])
+        self.assertEqual(resp['_status']['code'], status_code)

tests/test_api.py

@@ -19,7 +19,9 @@ class TestAPI:
         ('/demographics/123', 'GET', 404),
         ('/participants', 'GET', 200),
         ('/persons', 'GET', 404),
-        ('/participants/123', 'GET', 404)
+        ('/participants/123', 'GET', 404),
+        ('/studies', 'GET', 200),
+        ('/studies/123', 'GET', 404)
     ])
     def test_status_codes(self, client, endpoint, method, status_code):
         """ Test endpoint response codes """
@@ -47,7 +49,11 @@ def test_status_codes(self, client, endpoint, method, status_code):
         ('/participants', 'GET', 'success'),
         ('/participants/123', 'GET', 'could not find participant `123`'),
         ('/participants/123', 'PATCH', 'could not find participant `123`'),
-        ('/participants/123', 'DELETE', 'could not find participant `123`')
+        ('/participants/123', 'DELETE', 'could not find participant `123`'),
+        ('/studies', 'GET', 'success'),
+        ('/studies/123', 'GET', 'could not find study `123`'),
+        ('/studies/123', 'PATCH', 'could not find study `123`'),
+        ('/studies/123', 'DELETE', 'could not find study `123`'),
     ])
     def test_status_messages(self, client, endpoint, method, status_message):
         """
@@ -63,7 +69,8 @@ def test_status_messages(self, client, endpoint, method, status_message):
         ('/participants', 'GET'),
         ('/samples', 'GET'),
         ('/diagnoses', 'GET'),
-        ('/demographics', 'GET')
+        ('/demographics', 'GET'),
+        ('/studies', 'GET')
     ])
     def test_status_format(self, client, endpoint, method):
         """ Test that the _response field is consistent """
@@ -80,7 +87,9 @@ def test_status_format(self, client, endpoint, method):
         ('/participants', 'PATCH', ['created_at', 'modified_at']),
         ('/demographics', 'PATCH', ['created_at', 'modified_at']),
         ('/diagnoses', 'PATCH', ['created_at', 'modified_at']),
-        ('/samples', 'PATCH', ['created_at', 'modified_at'])
+        ('/samples', 'PATCH', ['created_at', 'modified_at']),
+        ('/studies', 'PATCH', ['created_at', 'modified_at']),
+        ('/studies', 'PATCH', ['created_at', 'modified_at'])
     ])
     def test_read_only(self, client, entities, endpoint, method, fields):
         """ Test that given fields can not be written or modified """
@@ -103,7 +112,8 @@ def test_read_only(self, client, entities, endpoint, method, fields):
     @pytest.mark.parametrize('endpoint', ['/participants',
                                           '/demographics',
                                           '/diagnoses',
-                                          '/samples'])
+                                          '/samples',
+                                          '/studies'])
     def test_unknown_field(self, client, entities, endpoint, method):
         """ Test that unknown fields are rejected when trying to create  """
         inputs = entities[endpoint]

tests/test_pagination.py

@@ -3,6 +3,7 @@
 from dateutil import parser
 
 from dataservice.extensions import db
+from dataservice.api.study.models import Study
 from dataservice.api.participant.models import Participant
 from dataservice.api.demographic.models import Demographic
 from dataservice.api.sample.models import Sample
@@ -17,6 +18,13 @@ class TestPagination:
 
     @pytest.fixture(scope='module')
     def participants(client):
+
+        # Add a bunch of studies for pagination
+        for _ in range(101):
+            s = Study(external_id='blah')
+            db.session.add(s)
+        db.session.commit()
+
         s = Study(external_id='blah', name='test')
         db.session.add(s)
         db.session.flush()
@@ -38,6 +46,7 @@ def participants(client):
         ('/demographics'),
         ('/samples'),
         ('/diagnoses'),
+        ('/studies'),
     ])
     def test_pagination(self, client, participants, endpoint):
         """ Test pagination of resource """
@@ -69,6 +78,7 @@ def test_pagination(self, client, participants, endpoint):
         ('/demographics'),
         ('/samples'),
         ('/diagnoses'),
+        ('/studies'),
     ])
     def test_limit(self, client, participants, endpoint):
         # Check that limit param operates correctly
@@ -92,6 +102,7 @@ def test_limit(self, client, participants, endpoint):
         ('/demographics'),
         ('/samples'),
         ('/diagnoses'),
+        ('/studies'),
     ])
     def test_after(self, client, participants, endpoint):
         """ Test `after` offeset paramater """
@@ -120,6 +131,7 @@ def test_after(self, client, participants, endpoint):
         ('/demographics'),
         ('/samples'),
         ('/diagnoses'),
+        ('/studies'),
     ])
     def test_self(self, client, participants, endpoint):
         """ Test that the self link gives the same page """