✅ Add tests for GenomicFile

Create mocks for indexd

config.py

@@ -44,6 +44,8 @@ class TestingConfig(Config):
     SQLALCHEMY_DATABASE_URI = 'postgres://postgres@localhost:5432/test'
     SQLALCHEMY_TRACK_MODIFICATIONS = True
 
+    INDEXD_URL = os.environ.get('INDEXD_URL', '')
+
 
 class ProductionConfig(Config):
     @staticmethod

dataservice/api/genomic_file/models.py

@@ -78,8 +78,9 @@ def merge_indexd(self):
         """
         Gets additional fields from indexd
         """
-        if current_app.config['DEBUG']:
+        if current_app.config['INDEXD_URL'] == None:
             return
+
         indexd_url = current_app.config['INDEXD_URL']
         resp = requests.get(indexd_url + self.uuid)
         for prop, v in resp.json().items():

dataservice/api/genomic_file/resources.py

@@ -3,6 +3,7 @@
 from marshmallow import ValidationError
 
 from dataservice.extensions import db
+from dataservice.api.common.pagination import paginated, Pagination
 from dataservice.api.genomic_file.models import GenomicFile
 from dataservice.api.genomic_file.schemas import GenomicFileSchema
 from dataservice.api.common.views import CRUDView
@@ -16,9 +17,13 @@ class GenomicFileListAPI(CRUDView):
     rule = '/genomic-files'
     schemas = {'GenomicFile': GenomicFileSchema}
 
-    def get(self):
+    @paginated
+    def get(self, after, limit):
         """
-        Get a paginated genomic_files
+        Get paginated genomic_files
+
+        Retrieves the genomic files stored in the datamodel, then fetch
+        additional properties that are stored in indexd under the same uuid.
         ---
         template:
           path:
@@ -103,9 +108,8 @@ def put(self, kf_id):
               GenomicFile
         """
         body = request.json or {}
-        try:
-            gf = GenomicFile.query.get(kf_id)
-        except NoResultFound:
+        gf = GenomicFile.query.get(kf_id)
+        if gf is None:
             abort(404, 'could not find {} `{}`'
                   .format('GenomicFile', kf_id))
 

dataservice/api/genomic_file/schemas.py

@@ -6,7 +6,6 @@
 
 
 class GenomicFileSchema(BaseSchema):
-    __endpoint__ = 'api.genomic_files'
     class Meta(BaseSchema.Meta):
         model = GenomicFile
         resource_url = 'api.genomic_files'

dev-requirements.txt

@@ -3,3 +3,4 @@ pytest==3.3.1
 pytest-cache==1.0
 pytest-cov==2.5.1
 pytest-pep8==1.0.6
+pytest-mock==1.7.0

tests/conftest.py

@@ -19,6 +19,8 @@
 from dataservice.api.sequencing_experiment.models import SequencingExperiment
 from dataservice.api.study_file.models import StudyFile
 
+from tests.mocks import MockIndexd
+
 
 @pytest.yield_fixture(scope='session')
 def app():
@@ -36,13 +38,17 @@ def client(app):
     db.drop_all()
 
 
-@pytest.yield_fixture(scope='module')
+@pytest.yield_fixture(scope='function')
 def swagger(client):
     yield json.loads(client.get('/swagger').data.decode('utf-8'))
 
 
 @pytest.fixture
-def entities(client):
+def entities(client, mocker):
+    mock = mocker.patch('dataservice.api.genomic_file.models.requests')
+    indexd = MockIndexd()
+    mock.get = indexd.get
+    mock.post = indexd.post
     """
     Create mock entities
     """
@@ -55,6 +61,7 @@ def entities(client):
             'data_type': 'reads',
             'file_format': 'fastq',
             'file_url': 's3://bucket/key',
+            'urls': ['s3://bucket/key'],
             'md5sum': str(uuid.uuid4()),
             'controlled_access': False
         },
@@ -91,16 +98,10 @@ def entities(client):
             'shipment_origin': 'CORIELL',
             'shipment_destination': 'Baylor',
             'analyte_type': 'DNA',
-<<<<<<< HEAD
             'concentration_mg_per_ml': 200.0,
             'volume_ml': 13.99,
             'shipment_date': str(datetime.utcnow()),
             'uberon_id': 'test'
-=======
-            'concentration': 200,
-            'volume': 13.99,
-            'shipment_date': str(datetime.utcnow()),
->>>>>>> :sparkles: Add genomic file resource
         },
         '/sequencing-experiments': {
             'external_id': 'se1',
@@ -178,19 +179,9 @@ def entities(client):
                            biospecimen_id=biospecimen.kf_id,
                            sequencing_experiment_id=seq_exp.kf_id)
 
-<<<<<<< HEAD
     biospecimen.genomic_files = [gen_file]
     seq_exp.genomic_files = [gen_file]
     p.biospecimens = [biospecimen]
-=======
-    aliquot.sequencing_experiments = [seq_exp]
-    sample.aliquots = [aliquot]
-    genomic_file = GenomicFile(**inputs['/genomic-files'])
-    sample.aliquots = [aliquot]
-    p.samples = [sample]
-    sample.aliquots = [aliquot]
-    aliquot.sequencing_experiments = [seq_exp]
->>>>>>> :sparkles: Add genomic file resource
     p.diagnoses = [diagnosis]
     p.outcomes = [outcome]
     p.phenotypes = [phenotype]

tests/genomic_file/test_genomic_file_models.py

@@ -2,14 +2,18 @@
 import random
 
 from sqlalchemy.exc import IntegrityError
+from unittest.mock import patch
 
 from dataservice.extensions import db
 from dataservice.api.study.models import Study
 from dataservice.api.participant.models import Participant
 from dataservice.api.biospecimen.models import Biospecimen
 from dataservice.api.sequencing_experiment.models import SequencingExperiment
 from dataservice.api.genomic_file.models import GenomicFile
+
 from tests.utils import FlaskTestCase
+from tests.mocks import MockIndexd
+
 
 MAX_SIZE_MB = 5000
 MIN_SIZE_MB = 1000
@@ -21,10 +25,13 @@ class ModelTest(FlaskTestCase):
     Test GenomicFile database model
     """
 
-    def test_create_and_find(self):
+    @patch('dataservice.api.genomic_file.models.requests')
+    def test_create_and_find(self, mock):
         """
         Test create genomic file
         """
+        indexd = MockIndexd()
+        mock.post = indexd.post
         # Create genomic file dependent entities
         self._create_save_dependents()
 
@@ -42,7 +49,7 @@ def test_create_and_find(self):
                 'data_type': 'submitted aligned read',
                 'file_format': '.cram',
                 'file_url': 's3://file_{}'.format(i),
-                'md5sum': str(uuid.uuid4()),
+                'md5sum': uuid.uuid4(),
                 'controlled_access': True,
                 'is_harmonized': True,
                 'reference_genome': 'Test01',
@@ -66,10 +73,13 @@ def test_create_and_find(self):
             for k, v in kwargs.items():
                 self.assertEqual(getattr(gf, k), v)
 
+    @patch('dataservice.api.genomic_file.models.requests')
     def test_create_via_biospecimen(self):
         """
         Test create genomic file
         """
+        indexd = MockIndexd()
+        mock.post = indexd.post
         # Create and save genomic files and dependent entities
         biospecimen_id, kwargs_dict = self._create_save_genomic_files()
 
@@ -87,10 +97,13 @@ def test_create_via_biospecimen(self):
             for k, v in kwargs.items():
                 self.assertEqual(getattr(gf, k), v)
 
-    def test_update(self):
+    @patch('dataservice.api.genomic_file.models.requests')
+    def test_update(self, mock):
         """
         Test update genomic file
         """
+        indexd = MockIndexd()
+        mock.post = indexd.post
         # Create and save genomic files and dependent entities
         biospecimen_id, kwargs_dict = self._create_save_genomic_files()
 
@@ -108,10 +121,13 @@ def test_update(self):
         [self.assertEqual(getattr(gf, k), v)
          for k, v in kwargs.items()]
 
-    def test_delete(self):
+    @patch('dataservice.api.genomic_file.models.requests')
+    def test_delete(self, mock):
         """
         Test delete existing genomic file
         """
+        indexd = MockIndexd()
+        mock.post = indexd.post
         # Create and save genomic files and dependent entities
         biospecimen_id, kwargs_dict = self._create_save_genomic_files()
 
@@ -129,12 +145,15 @@ def test_delete(self):
             kf_id=biospecimen_id).one()
         self.assertEqual(len(biospecimen.genomic_files), 0)
 
+    @patch('dataservice.api.genomic_file.models.requests')
     def test_delete_via_biospecimen(self):
         """
         Test delete existing genomic file
 
         Delete biospecimen to which genomic file belongs
         """
+        indexd = MockIndexd()
+        mock.post = indexd.post
         # Create and save genomic files and dependent entities
         biospecimen_id, kwargs_dict = self._create_save_genomic_files()
 

tests/genomic_file/test_genomic_file_resources.py

@@ -10,23 +10,28 @@
 from dataservice.extensions import db
 from dataservice.api.genomic_file.models import GenomicFile
 
-from tests.mocks import mock_indexd_post, mock_indexd_get, mock_indexd_put
+from tests.mocks import MockIndexd
 
 
 GENOMICFILE_URL = 'api.genomic_files'
 GENOMICFILE_LIST_URL = 'api.genomic_files_list'
 
 
 @pytest.fixture
-def genomic_files(client):
+def genomic_files(client, mocker):
+    mock = mocker.patch('dataservice.api.genomic_file.models.requests')
+    indexd = MockIndexd()
+    mock.get = indexd.get
+    mock.post = indexd.post
+
     props = {
         'file_name': 'hg38.bam',
         'data_type': 'aligned reads',
         'file_format': 'bam'
     }
-    db.session.add(participant)
     gfs = [GenomicFile(**props) for _ in range(102)]
     db.session.add_all(gfs)
+    db.session.commit()
 
 
 def test_new(client, mocker):
@@ -35,12 +40,12 @@ def test_new(client, mocker):
     """
     # Mock data returned from gen3
     mock = mocker.patch('dataservice.api.genomic_file.models.requests')
-    mock.post = mock_indexd_post()
+    mock.post = MockIndexd().post
 
     resp = _new_genomic_file(client)
     assert 'genomic_file' in resp['_status']['message']
     assert 'created' in resp['_status']['message']
-    assert GenomicFile.query.first().uuid == mock_indexd_post()().json()['did']
+    assert resp['results']['file_name'] == 'hg38.bam'
 
     gf = GenomicFile.query.first()
     genomic_file = resp['results']
@@ -53,7 +58,7 @@ def test_new_indexd_error(client, mocker):
     """
     # Mock data returned from gen3
     mock = mocker.patch('dataservice.api.genomic_file.models.requests')
-    mock.post = mock_indexd_post(status_code=500)
+    mock.post = MockIndexd(status_code=500).post
 
     body = {
         'file_name': 'hg38.bam',
@@ -81,14 +86,17 @@ def test_get_list(client, genomic_files, mocker):
     """
     # Mock data returned from gen3
     mock = mocker.patch('dataservice.api.genomic_file.models.requests')
-    mock.get = mock_indexd_get
+    indexd = MockIndexd()
+    mock.get = indexd.get
+    mock.post = indexd.post
 
     resp = client.get(url_for(GENOMICFILE_LIST_URL))
     resp = json.loads(resp.data.decode('utf-8'))
 
     assert resp['_status']['code'] == 200
     assert resp['total'] == 102
     assert len(resp['results']) == 10
+    # Check that each entry has both the model's and indexd's fields
     for r in resp['results']:
         assert r['hashes'] == {'md5': 'dcff06ebb19bc9aa8f1aae1288d10dc2'}
         assert r['metadata'] == {'acls': 'INTERNAL'}
@@ -106,7 +114,8 @@ def test_get_one(client, genomic_files, mocker):
     """
     # Mock data returned from gen3
     mock = mocker.patch('dataservice.api.genomic_file.models.requests')
-    mock.get = mock_indexd_get
+    indexd = MockIndexd()
+    mock.get = indexd.get
 
     gf = GenomicFile.query.first()
 
@@ -125,14 +134,16 @@ def test_get_one(client, genomic_files, mocker):
     assert resp['data_type'] == 'aligned reads'
     assert resp['file_format'] == 'bam'
 
+
 def test_update(client, mocker):
     """
     Test updating an existing genomic file
     """
     mock = mocker.patch('dataservice.api.genomic_file.models.requests')
-    mock.get = mock_indexd_get
-    mock.post = mock_indexd_post()
-    mock.put = mock_indexd_put()
+    indexd = MockIndexd()
+    mock.post = indexd.post
+    mock.get = indexd.get
+    mock.put = indexd.put
 
     resp = _new_genomic_file(client)
     participant = resp['results']
@@ -147,7 +158,7 @@ def test_update(client, mocker):
                                data=json.dumps(body),
                           headers={'Content-Type': 'application/json'})
 
-    assert response.status_code == 201
+    assert response.status_code == 200
 
     resp = json.loads(response.data.decode("utf-8"))
     assert 'genomic_file' in resp['_status']['message']
@@ -166,8 +177,9 @@ def test_delete(client, mocker):
     Test deleting a participant by id
     """
     mock = mocker.patch('dataservice.api.genomic_file.models.requests')
-    mock.post = mock_indexd_get()
-    mock.post = mock_indexd_post()
+    indexd = MockIndexd()
+    mock.get = indexd.get
+    mock.post = indexd.post
 
     init = GenomicFile.query.count()
 
@@ -191,8 +203,9 @@ def test_delete_error(client, mocker):
     Test handling of indexd error
     """
     mock = mocker.patch('dataservice.api.genomic_file.models.requests')
-    mock.post = mock_indexd_get()
-    mock.post = mock_indexd_post()
+    indexd = MockIndexd()
+    mock.get = indexd.get
+    mock.post = indexd.post
 
     response_mock = MagicMock()
     response_mock.status_code = 500