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Code Issues Packages Projects Releases Wiki Activity

config refactor (#1854)

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* split out config

* add tests for base and app config, refactor client config out of app config

* refactor default config retrieval

* create config test class and helper functions

* move default_config into server to fix import issue
This commit is contained in:
Madison Dunitz
2020-09-29 16:42:46 -05:00
committed by GitHub
parent 1145f61c78
commit af3c6e1d8e
57 changed files with 2667 additions and 1599 deletions
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server/test/unit/common/test_writable_annotation.py
+7 -9
View File
@@ -27,7 +27,7 @@ class auth(object):
class WritableTileDBStoredAnnotationTest(unittest.TestCase):
def setUp(self):
self.user_id = '1234'
self.user_id = "1234"
self.data, self.tmp_dir, self.annotations = data_with_tmp_tiledb_annotations(MatrixDataType.H5AD)
self.data.dataset_config.user_annotations = self.annotations
self.db = self.annotations.db
@@ -38,7 +38,7 @@ class WritableTileDBStoredAnnotationTest(unittest.TestCase):
}
self.fbs = make_fbs(self.test_dict)
self.df = pd.DataFrame(self.test_dict)
self.app = Flask('fake_app')
self.app = Flask("fake_app")
self.app.__setattr__("auth", auth)
def tearDown(self):
@@ -65,8 +65,7 @@ class WritableTileDBStoredAnnotationTest(unittest.TestCase):
self.annotations.write_labels(self.df, self.data)
dataset_id = self.db.query([CellxGeneDataset], [CellxGeneDataset.name == self.data.get_location()])[0].id
annotation = self.db.query_for_most_recent(
Annotation,
[Annotation.user_id == self.user_id, Annotation.dataset_id == str(dataset_id)]
Annotation, [Annotation.user_id == self.user_id, Annotation.dataset_id == str(dataset_id)]
)
# retrieve tiledb array
df = tiledb.open(annotation.tiledb_uri)
@@ -78,7 +77,7 @@ class WritableTileDBStoredAnnotationTest(unittest.TestCase):
def test_write_labels_creates_a_dataset_if_it_doesnt_exist(self):
with self.app.test_request_context():
new_name = 'new_dataset/location'
new_name = "new_dataset/location"
self.data.get_location = MagicMock(return_value=new_name)
num_datasets = len(self.db.query([CellxGeneDataset]))
self.annotation_put_fbs(self.fbs)
@@ -130,15 +129,14 @@ class WritableTileDBStoredAnnotationTest(unittest.TestCase):
with self.assertRaises(KeyError):
self.annotation_put_fbs(fbs_bad)
@patch('server.common.annotations.hosted_tiledb.current_app')
@patch("server.common.annotations.hosted_tiledb.current_app")
def test_write_labels_stores_df_as_tiledb_array(self, mock_user_id):
mock_user_id.auth.get_user_id.return_value = '1234'
mock_user_id.auth.get_user_id.return_value = "1234"
self.annotations.write_labels(self.df, self.data)
# get uri
dataset_id = self.db.query([CellxGeneDataset], [CellxGeneDataset.name == self.data.get_location()])[0].id
annotation = self.db.query_for_most_recent(
Annotation,
[Annotation.user_id == '1234', Annotation.dataset_id == str(dataset_id)]
Annotation, [Annotation.user_id == "1234", Annotation.dataset_id == str(dataset_id)]
)
df = tiledb.open(annotation.tiledb_uri)