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Code Issues Packages Projects Releases Wiki Activity

do not hard-wire column names in annotations (#785)

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* enforce column name uniqueness for obs and var

* parameterize the column name containing obs and var user-readable names

* use the new annotation index value from schema

* update f/e unit tests

* PR review suggestions

* lint
This commit is contained in:
Bruce Martin
2019-05-24 21:00:54 -07:00
committed by GitHub
parent a8c2e408d1
commit 3dc45d6330
16 changed files with 246 additions and 155 deletions
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server/test/test_api.py
+10 -5
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@@ -23,7 +23,8 @@ class EndPoints(unittest.TestCase):
session = requests.Session()
for i in range(90):
try:
session.get(f"{URL_BASE}schema")
result = session.get(f"{URL_BASE}schema")
cls.schema = result.json()
except requests.exceptions.ConnectionError:
time.sleep(1)
@@ -45,7 +46,8 @@ class EndPoints(unittest.TestCase):
self.assertEqual(result.headers["Content-Type"], "application/json")
result_data = result.json()
self.assertEqual(result_data["schema"]["dataframe"]["nObs"], 2638)
self.assertEqual(len(result_data["schema"]["annotations"]["obs"]), 5)
self.assertEqual(len(result_data["schema"]["annotations"]["obs"]), 2)
self.assertEqual(len(result_data["schema"]["annotations"]["obs"]["columns"]), 5)
def test_config(self):
endpoint = "config"
@@ -95,7 +97,8 @@ class EndPoints(unittest.TestCase):
self.assertIsNotNone(df['col_idx'])
self.assertIsNone(df['row_idx'])
self.assertEqual(len(df['columns']), df['n_cols'])
self.assertListEqual(df['col_idx'], ['name', 'n_genes', 'percent_mito', 'n_counts', 'louvain'])
obs_index_col_name = self.schema["schema"]["annotations"]["obs"]["index"]
self.assertListEqual(df['col_idx'], [obs_index_col_name, 'n_genes', 'percent_mito', 'n_counts', 'louvain'])
def test_get_annotations_obs_keys_fbs(self):
endpoint = "annotations/obs"
@@ -165,7 +168,8 @@ class EndPoints(unittest.TestCase):
self.assertIsNotNone(df['col_idx'])
self.assertIsNone(df['row_idx'])
self.assertEqual(len(df['columns']), df['n_cols'])
self.assertListEqual(df['col_idx'], ['name', 'n_cells'])
var_index_col_name = self.schema["schema"]["annotations"]["var"]["index"]
self.assertListEqual(df['col_idx'], [var_index_col_name, 'n_cells'])
def test_get_annotations_var_keys_fbs(self):
endpoint = "annotations/var"
@@ -247,7 +251,8 @@ class EndPoints(unittest.TestCase):
endpoint = f"data/var"
url = f"{URL_BASE}{endpoint}"
header = {"Accept": "application/octet-stream"}
var_filter = {"filter": {"var": {"annotation_value": [{"name": "name", "values": ["RER1"]}]}}}
index_col_name = self.schema["schema"]["annotations"]["var"]["index"]
var_filter = {"filter": {"var": {"annotation_value": [{"name": index_col_name, "values": ["RER1"]}]}}}
result = self.session.put(url, headers=header, json=var_filter)
self.assertEqual(result.status_code, HTTPStatus.OK)
self.assertEqual(result.headers["Content-Type"], "application/octet-stream")