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Apply yapf to python files

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This commit is contained in:
Matt Weiden
2019-12-19 15:20:41 -08:00
parent 42a8d45bd7
commit cdca128a01
43 changed files with 1143 additions and 678 deletions
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server/test/test_api.py
+80 -28
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@@ -19,7 +19,10 @@ class EndPoints(unittest.TestCase):
@classmethod
def setUpClass(cls):
cls.ps = Popen(["cellxgene", "launch", "../example-dataset/pbmc3k.h5ad", "--verbose", "--port", "5005"])
cls.ps = Popen([
"cellxgene", "launch", "../example-dataset/pbmc3k.h5ad",
"--verbose", "--port", "5005"
])
session = requests.Session()
for i in range(90):
try:
@@ -47,7 +50,8 @@ class EndPoints(unittest.TestCase):
result_data = result.json()
self.assertEqual(result_data["schema"]["dataframe"]["nObs"], 2638)
self.assertEqual(len(result_data["schema"]["annotations"]["obs"]), 2)
self.assertEqual(len(result_data["schema"]["annotations"]["obs"]["columns"]), 5)
self.assertEqual(
len(result_data["schema"]["annotations"]["obs"]["columns"]), 5)
def test_config(self):
endpoint = "config"
@@ -57,7 +61,8 @@ class EndPoints(unittest.TestCase):
self.assertEqual(result.headers["Content-Type"], "application/json")
result_data = result.json()
self.assertIn("library_versions", result_data["config"])
self.assertEqual(result_data["config"]["displayNames"]["dataset"], "pbmc3k")
self.assertEqual(result_data["config"]["displayNames"]["dataset"],
"pbmc3k")
self.assertEqual(len(result_data["config"]["features"]), 4)
def test_get_layout_fbs(self):
@@ -66,13 +71,15 @@ class EndPoints(unittest.TestCase):
header = {"Accept": "application/octet-stream"}
result = self.session.get(url, headers=header)
self.assertEqual(result.status_code, HTTPStatus.OK)
self.assertEqual(result.headers["Content-Type"], "application/octet-stream")
self.assertEqual(result.headers["Content-Type"],
"application/octet-stream")
df = decode_fbs.decode_matrix_FBS(result.content)
self.assertEqual(df['n_rows'], 2638)
self.assertEqual(df['n_cols'], 8)
self.assertIsNotNone(df['columns'])
self.assertListEqual(df['col_idx'], [
'pca_0', 'pca_1', 'tsne_0', 'tsne_1', 'umap_0', 'umap_1', 'draw_graph_fr_0', 'draw_graph_fr_1'
'pca_0', 'pca_1', 'tsne_0', 'tsne_1', 'umap_0', 'umap_1',
'draw_graph_fr_0', 'draw_graph_fr_1'
])
self.assertIsNone(df['row_idx'])
self.assertEqual(len(df['columns']), df['n_cols'])
@@ -89,7 +96,8 @@ class EndPoints(unittest.TestCase):
header = {"Accept": "application/octet-stream"}
result = self.session.get(url, headers=header)
self.assertEqual(result.status_code, HTTPStatus.OK)
self.assertEqual(result.headers["Content-Type"], "application/octet-stream")
self.assertEqual(result.headers["Content-Type"],
"application/octet-stream")
df = decode_fbs.decode_matrix_FBS(result.content)
self.assertEqual(df['n_rows'], 2638)
self.assertEqual(df['n_cols'], 5)
@@ -97,8 +105,11 @@ class EndPoints(unittest.TestCase):
self.assertIsNotNone(df['col_idx'])
self.assertIsNone(df['row_idx'])
self.assertEqual(len(df['columns']), df['n_cols'])
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'])
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"
@@ -107,7 +118,8 @@ class EndPoints(unittest.TestCase):
header = {"Accept": "application/octet-stream"}
result = self.session.get(url, headers=header)
self.assertEqual(result.status_code, HTTPStatus.OK)
self.assertEqual(result.headers["Content-Type"], "application/octet-stream")
self.assertEqual(result.headers["Content-Type"],
"application/octet-stream")
df = decode_fbs.decode_matrix_FBS(result.content)
self.assertEqual(df['n_rows'], 2638)
self.assertEqual(df['n_cols'], 2)
@@ -129,8 +141,26 @@ class EndPoints(unittest.TestCase):
url = f"{URL_BASE}{endpoint}"
params = {
"mode": "topN",
"set1": {"filter": {"obs": {"annotation_value": [{"name": "louvain", "values": ["NK cells"]}]}}},
"set2": {"filter": {"obs": {"annotation_value": [{"name": "louvain", "values": ["CD8 T cells"]}]}}},
"set1": {
"filter": {
"obs": {
"annotation_value": [{
"name": "louvain",
"values": ["NK cells"]
}]
}
}
},
"set2": {
"filter": {
"obs": {
"annotation_value": [{
"name": "louvain",
"values": ["CD8 T cells"]
}]
}
}
},
"count": 7,
}
result = self.session.post(url, json=params)
@@ -145,8 +175,20 @@ class EndPoints(unittest.TestCase):
params = {
"mode": "topN",
"count": 10,
"set1": {"filter": {"obs": {"index": [[0, 500]]}}},
"set2": {"filter": {"obs": {"index": [[500, 1000]]}}},
"set1": {
"filter": {
"obs": {
"index": [[0, 500]]
}
}
},
"set2": {
"filter": {
"obs": {
"index": [[500, 1000]]
}
}
},
}
result = self.session.post(url, json=params)
self.assertEqual(result.status_code, HTTPStatus.OK)
@@ -160,7 +202,8 @@ class EndPoints(unittest.TestCase):
header = {"Accept": "application/octet-stream"}
result = self.session.get(url, headers=header)
self.assertEqual(result.status_code, HTTPStatus.OK)
self.assertEqual(result.headers["Content-Type"], "application/octet-stream")
self.assertEqual(result.headers["Content-Type"],
"application/octet-stream")
df = decode_fbs.decode_matrix_FBS(result.content)
self.assertEqual(df['n_rows'], 1838)
self.assertEqual(df['n_cols'], 2)
@@ -168,7 +211,8 @@ class EndPoints(unittest.TestCase):
self.assertIsNotNone(df['col_idx'])
self.assertIsNone(df['row_idx'])
self.assertEqual(len(df['columns']), df['n_cols'])
var_index_col_name = self.schema["schema"]["annotations"]["var"]["index"]
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):
@@ -178,7 +222,8 @@ class EndPoints(unittest.TestCase):
header = {"Accept": "application/octet-stream"}
result = self.session.get(url, headers=header)
self.assertEqual(result.status_code, HTTPStatus.OK)
self.assertEqual(result.headers["Content-Type"], "application/octet-stream")
self.assertEqual(result.headers["Content-Type"],
"application/octet-stream")
df = decode_fbs.decode_matrix_FBS(result.content)
self.assertEqual(df['n_rows'], 1838)
self.assertEqual(df['n_cols'], 1)
@@ -207,7 +252,8 @@ class EndPoints(unittest.TestCase):
url = f"{URL_BASE}{endpoint}"
result = self.session.put(url)
self.assertEqual(result.status_code, HTTPStatus.OK)
self.assertEqual(result.headers["Content-Type"], "application/octet-stream")
self.assertEqual(result.headers["Content-Type"],
"application/octet-stream")
def test_data_put_fbs(self):
endpoint = f"data/var"
@@ -215,7 +261,8 @@ class EndPoints(unittest.TestCase):
header = {"Accept": "application/octet-stream"}
result = self.session.put(url, headers=header)
self.assertEqual(result.status_code, HTTPStatus.OK)
self.assertEqual(result.headers["Content-Type"], "application/octet-stream")
self.assertEqual(result.headers["Content-Type"],
"application/octet-stream")
df = decode_fbs.decode_matrix_FBS(result.content)
self.assertEqual(df['n_rows'], 2638)
self.assertEqual(df['n_cols'], 1838)
@@ -228,16 +275,11 @@ class EndPoints(unittest.TestCase):
endpoint = f"data/var"
url = f"{URL_BASE}{endpoint}"
header = {"Accept": "application/octet-stream"}
filter = {
"filter": {
"var": {
"index": [0, 1, 4]
}
}
}
filter = {"filter": {"var": {"index": [0, 1, 4]}}}
result = self.session.put(url, headers=header, json=filter)
self.assertEqual(result.status_code, HTTPStatus.OK)
self.assertEqual(result.headers["Content-Type"], "application/octet-stream")
self.assertEqual(result.headers["Content-Type"],
"application/octet-stream")
df = decode_fbs.decode_matrix_FBS(result.content)
self.assertEqual(df['n_rows'], 2638)
self.assertEqual(df['n_cols'], 3)
@@ -252,10 +294,20 @@ class EndPoints(unittest.TestCase):
url = f"{URL_BASE}{endpoint}"
header = {"Accept": "application/octet-stream"}
index_col_name = self.schema["schema"]["annotations"]["var"]["index"]
var_filter = {"filter": {"var": {"annotation_value": [{"name": index_col_name, "values": ["RER1"]}]}}}
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")
self.assertEqual(result.headers["Content-Type"],
"application/octet-stream")
df = decode_fbs.decode_matrix_FBS(result.content)
self.assertEqual(df["n_rows"], 2638)
self.assertEqual(df["n_cols"], 1)