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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/converters/test_h5ad_data_file.py
+54 -21
View File
@@ -16,7 +16,6 @@ PROJECT_ROOT = popen("git rev-parse --show-toplevel").read().strip()
class TestH5ADDataFile(unittest.TestCase):
def setUp(self):
self.sample_anndata = self._create_sample_anndata_dataset()
self.sample_h5ad_filename = self._write_anndata_to_file(self.sample_anndata)
@@ -40,8 +39,12 @@ class TestH5ADDataFile(unittest.TestCase):
def test__create_h5ad_data_file__assert_warning_outputted_if_dataset_title_or_about_given(self):
with self.assertLogs(level="WARN") as logger:
H5ADDataFile(self.sample_h5ad_filename, dataset_title="My Awesome Dataset",
dataset_about="http://www.awesomedataset.com", use_corpora_schema=False)
H5ADDataFile(
self.sample_h5ad_filename,
dataset_title="My Awesome Dataset",
dataset_about="http://www.awesomedataset.com",
use_corpora_schema=False,
)
self.assertIn("will override any metadata that is extracted", logger.output[0])
@@ -49,10 +52,12 @@ class TestH5ADDataFile(unittest.TestCase):
h5ad_file = H5ADDataFile(self.sample_h5ad_filename, use_corpora_schema=False)
self.assertTrue((h5ad_file.anndata.X == self.sample_anndata.X).all())
self.assertEqual(h5ad_file.anndata.obs.sort_index(inplace=True),
self.sample_anndata.obs.sort_index(inplace=True))
self.assertEqual(h5ad_file.anndata.var.sort_index(inplace=True),
self.sample_anndata.var.sort_index(inplace=True))
self.assertEqual(
h5ad_file.anndata.obs.sort_index(inplace=True), self.sample_anndata.obs.sort_index(inplace=True)
)
self.assertEqual(
h5ad_file.anndata.var.sort_index(inplace=True), self.sample_anndata.var.sort_index(inplace=True)
)
for key in h5ad_file.anndata.obsm.keys():
self.assertIn(key, self.sample_anndata.obsm.keys())
@@ -73,8 +78,12 @@ class TestH5ADDataFile(unittest.TestCase):
self.assertIn("name_0", h5ad_file.var.columns)
def test__create_h5ad_data_file__no_copy_if_obs_and_var_index_names_specified(self):
h5ad_file = H5ADDataFile(self.sample_h5ad_filename, use_corpora_schema=False,
obs_index_column_name="float_category", vars_index_column_name="int_category")
h5ad_file = H5ADDataFile(
self.sample_h5ad_filename,
use_corpora_schema=False,
obs_index_column_name="float_category",
vars_index_column_name="int_category",
)
self.assertNotIn("name_0", h5ad_file.obs.columns)
self.assertNotIn("name_0", h5ad_file.var.columns)
@@ -82,15 +91,23 @@ class TestH5ADDataFile(unittest.TestCase):
def test__create_h5ad_data_file__obs_and_var_index_names_specified_not_unique_raises_exception(self):
with self.assertRaises(Exception) as exception_context:
H5ADDataFile(self.sample_h5ad_filename, use_corpora_schema=False,
obs_index_column_name="float_category", vars_index_column_name="bool_category")
H5ADDataFile(
self.sample_h5ad_filename,
use_corpora_schema=False,
obs_index_column_name="float_category",
vars_index_column_name="bool_category",
)
self.assertIn("Please prepare data to contain unique values", str(exception_context.exception))
def test__create_h5ad_data_file__obs_and_var_index_names_specified_doesnt_exist_raises_exception(self):
with self.assertRaises(Exception) as exception_context:
H5ADDataFile(self.sample_h5ad_filename, use_corpora_schema=False,
obs_index_column_name="unknown_category", vars_index_column_name="i_dont_exist")
H5ADDataFile(
self.sample_h5ad_filename,
use_corpora_schema=False,
obs_index_column_name="unknown_category",
vars_index_column_name="i_dont_exist",
)
self.assertIn("does not exist", str(exception_context.exception))
@@ -101,8 +118,9 @@ class TestH5ADDataFile(unittest.TestCase):
self.assertEqual(h5ad_file.dataset_about, "www.link.com")
def test__create_h5ad_data_file__inputted_dataset_title_and_about_overrides_extracted(self):
h5ad_file = H5ADDataFile(self.sample_h5ad_filename, dataset_about="override_about",
dataset_title="override_title")
h5ad_file = H5ADDataFile(
self.sample_h5ad_filename, dataset_about="override_about", dataset_title="override_title"
)
self.assertEqual(h5ad_file.dataset_title, "override_title")
self.assertEqual(h5ad_file.dataset_about, "override_about")
@@ -145,8 +163,11 @@ class TestH5ADDataFile(unittest.TestCase):
remove(sparse_with_column_shift_filename)
def _validate_expected_generated_list_of_tiledb_files(self, has_column_encoding=False):
expected_directories, expected_obs_files, expected_var_files = \
self._get_expected_generated_list_of_tiledb_files()
(
expected_directories,
expected_obs_files,
expected_var_files,
) = self._get_expected_generated_list_of_tiledb_files()
for directory in expected_directories:
self.assertTrue(path.isdir(directory))
@@ -187,8 +208,18 @@ class TestH5ADDataFile(unittest.TestCase):
var_files.append("bool_category.tdb")
var_files.append("int_category.tdb")
return [metadata_directory, main_x_directory, overall_embedding_directory, specific_embedding_directory,
obs_directory, var_directory], obs_files, var_files
return (
[
metadata_directory,
main_x_directory,
overall_embedding_directory,
specific_embedding_directory,
obs_directory,
var_directory,
],
obs_files,
var_files,
)
def _write_anndata_to_file(self, anndata):
temporary_filename = f"{PROJECT_ROOT}/server/test/fixtures/{uuid4()}.h5ad"
@@ -204,7 +235,8 @@ class TestH5ADDataFile(unittest.TestCase):
random_string_category = Series(data=["a", "b", "b"], dtype="category")
random_float_category = Series(data=[3.2, 1.1, 2.2], dtype=np.float32)
obs_dataframe = DataFrame(
data={"string_category": random_string_category, "float_category": random_float_category})
data={"string_category": random_string_category, "float_category": random_float_category}
)
obs = obs_dataframe
# Create vars
@@ -230,6 +262,7 @@ class TestH5ADDataFile(unittest.TestCase):
# Set project links to be a dictionary
uns["project_links"] = json.dumps(
[{"link_name": "random_link_name", "link_url": "www.link.com", "link_type": "SUMMARY"}])
[{"link_name": "random_link_name", "link_url": "www.link.com", "link_type": "SUMMARY"}]
)
return anndata.AnnData(X=X, obs=obs, var=var, obsm=obsm, uns=uns)