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Black -- formatter for python (#508)

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* Add black

* use black to format code

* Black version
This commit is contained in:
Charlotte Weaver
2018-12-12 09:44:47 -08:00
committed by GitHub
parent a847951658
commit 83154577e4
18 changed files with 636 additions and 791 deletions
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server/test/test_api.py
+59 -80
View File
@@ -9,15 +9,7 @@ LOCAL_URL = "http://127.0.0.1:5005/"
VERSION = "v0.2"
URL_BASE = f"{LOCAL_URL}api/{VERSION}/"
BAD_FILTER = {
"filter": {
"obs": {
"annotation_value": [
{"name": "xyz"},
],
}
}
}
BAD_FILTER = {"filter": {"obs": {"annotation_value": [{"name": "xyz"}]}}}
class EndPoints(unittest.TestCase):
@@ -133,7 +125,7 @@ class EndPoints(unittest.TestCase):
{"name": "louvain", "values": ["NK cells", "CD8 T cells"]},
{"name": "n_counts", "min": 3000},
],
"index": [1, 99, [1000, 2000]]
"index": [1, 99, [1000, 2000]],
}
}
}
@@ -154,7 +146,7 @@ class EndPoints(unittest.TestCase):
{"name": "louvain", "values": ["NK cells", "CD8 T cells"]},
{"name": "n_counts", "min": 3000},
],
"index": [1, 99, [1000, 2000]]
"index": [1, 99, [1000, 2000]],
}
}
}
@@ -170,23 +162,9 @@ 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"]}
]
}
}
},
"count": 7
"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)
self.assertEqual(result.status_code, HTTPStatus.OK)
@@ -199,20 +177,8 @@ 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)
@@ -249,15 +215,7 @@ class EndPoints(unittest.TestCase):
def test_put_annotations_var(self):
endpoint = "annotations/var"
url = f"{URL_BASE}{endpoint}"
var_filter = {
"filter": {
"var": {
"annotation_value": [
{"name": "name", "values": ["ATAD3C", "RER1"]},
]
}
}
}
var_filter = {"filter": {"var": {"annotation_value": [{"name": "name", "values": ["ATAD3C", "RER1"]}]}}}
result = self.session.put(url, json=var_filter)
self.assertEqual(result.status_code, HTTPStatus.OK)
result_data = result.json()
@@ -268,15 +226,7 @@ class EndPoints(unittest.TestCase):
endpoint = "annotations/var"
query = "annotation-name=n_cells"
url = f"{URL_BASE}{endpoint}?{query}"
var_filter = {
"filter": {
"var": {
"annotation_value": [
{"name": "name", "values": ["ATAD3C", "RER1"]},
]
}
}
}
var_filter = {"filter": {"var": {"annotation_value": [{"name": "name", "values": ["ATAD3C", "RER1"]}]}}}
result = self.session.put(url, json=var_filter)
self.assertEqual(result.status_code, HTTPStatus.OK)
result_data = result.json()
@@ -335,7 +285,7 @@ class EndPoints(unittest.TestCase):
{"name": "louvain", "values": ["NK cells", "CD8 T cells"]},
{"name": "n_counts", "min": 3000},
],
"index": [1, 99, [1000, 2000]]
"index": [1, 99, [1000, 2000]],
}
}
}
@@ -349,15 +299,7 @@ class EndPoints(unittest.TestCase):
endpoint = f"data/{axis}"
url = f"{URL_BASE}{endpoint}"
header = {"Accept": "application/json"}
var_filter = {
"filter": {
"var": {
"annotation_value": [
{"name": "name", "values": ["RER1"]},
]
}
}
}
var_filter = {"filter": {"var": {"annotation_value": [{"name": "name", "values": ["RER1"]}]}}}
result = self.session.put(url, headers=header, json=var_filter)
self.assertEqual(result.status_code, HTTPStatus.OK)
result_data = result.json()
@@ -371,16 +313,44 @@ class EndPoints(unittest.TestCase):
def test_cache(self):
endpoint = "annotations/var"
url = f"{URL_BASE}{endpoint}"
f1 = {"filter": {"var": {"annotation_value": [{"name": "name",
"values": ["HLA-DRB1", "HLA-DQA1", "HLA-DQB1", "HLA-DPA1",
"HLA-DPB1", "MS4A1", "IL32", "CCL5", "CD79B",
"CD79A"]}]}}}
f1 = {
"filter": {
"var": {
"annotation_value": [
{
"name": "name",
"values": [
"HLA-DRB1",
"HLA-DQA1",
"HLA-DQB1",
"HLA-DPA1",
"HLA-DPB1",
"MS4A1",
"IL32",
"CCL5",
"CD79B",
"CD79A",
],
}
]
}
}
}
result = self.session.put(url, json=f1)
self.assertEqual(result.status_code, HTTPStatus.OK)
result_data1 = result.json()
f2 = {"filter": {"var": {"annotation_value": [{"name": "name",
"values": ["FGFBP2", "GZMA", "LTB", "PRF1", "CTSW", "GZMH",
"CCL5", "CCL4", "CST7", "NKG7"]}]}}}
f2 = {
"filter": {
"var": {
"annotation_value": [
{
"name": "name",
"values": ["FGFBP2", "GZMA", "LTB", "PRF1", "CTSW", "GZMH", "CCL5", "CCL4", "CST7", "NKG7"],
}
]
}
}
}
result = self.session.put(url, json=f2)
self.assertEqual(result.status_code, HTTPStatus.OK)
result_data2 = result.json()
@@ -393,9 +363,18 @@ class EndPoints(unittest.TestCase):
result = self.session.put(url, json=f1)
self.assertEqual(result.status_code, HTTPStatus.OK)
result_data1 = result.json()
f2 = {"filter": {"var": {"annotation_value": [{"name": "name",
"values": ["FGFBP2", "GZMA", "LTB", "PRF1", "CTSW", "GZMH",
"CCL5", "CCL4", "CST7", "NKG7"]}]}}}
f2 = {
"filter": {
"var": {
"annotation_value": [
{
"name": "name",
"values": ["FGFBP2", "GZMA", "LTB", "PRF1", "CTSW", "GZMH", "CCL5", "CCL4", "CST7", "NKG7"],
}
]
}
}
}
result = self.session.put(url, json=f2)
self.assertEqual(result.status_code, HTTPStatus.OK)
result_data2 = result.json()
server/test/test_filter.py
+10 -8
View File
@@ -54,13 +54,17 @@ class UtilTest(unittest.TestCase):
def test_complex_filter(self):
filter_dict = ImmutableMultiDict(
[("obs:louvain", "NK cells"), ("obs:louvain", "CD8 T cells"), ("obs:n_counts", "3000,*")])
[("obs:louvain", "NK cells"), ("obs:louvain", "CD8 T cells"), ("obs:n_counts", "3000,*")]
)
filter_ = parse_filter(filter_dict, self.schema)
self.assertIn("obs", filter_)
self.assertEqual(filter_["obs"]["annotation_value"], [{"name": "louvain",
"values": ["NK cells", "CD8 T cells"]},
{"name": "n_counts",
"max": None, "min": 3000.0}])
self.assertEqual(
filter_["obs"]["annotation_value"],
[
{"name": "louvain", "values": ["NK cells", "CD8 T cells"]},
{"name": "n_counts", "max": None, "min": 3000.0},
],
)
def test_bad_filter(self):
bad_annotation_type = ImmutableMultiDict([("obs:tissue", "lung")])
@@ -71,9 +75,7 @@ class UtilTest(unittest.TestCase):
parse_filter(bad_axis, self.schema)
def test_boolean_filter(self):
schema = {
"obs": [{"name": "bool_filter", "type": "boolean"}]
}
schema = {"obs": [{"name": "bool_filter", "type": "boolean"}]}
filter_dict = ImmutableMultiDict([("obs:bool_filter", "false")])
filter_ = parse_filter(filter_dict, schema)
self.assertIn("obs", filter_)
server/test/test_scanpy_engine.py
+30 -101
View File
@@ -3,7 +3,6 @@ from os import path
import pytest
import time
import unittest
import argparse
import numpy as np
from pandas import Series
@@ -13,9 +12,15 @@ from server.app.scanpy_engine.scanpy_engine import ScanpyEngine
class UtilTest(unittest.TestCase):
def setUp(self):
args = {'layout': 'umap', 'diffexp': 'ttest', 'max_category_items': 100,
'obs_names': None, 'var_names': None, 'diffexp_lfc_cutoff': 0.01,
'nan_to_num': True}
args = {
"layout": "umap",
"diffexp": "ttest",
"max_category_items": 100,
"obs_names": None,
"var_names": None,
"diffexp_lfc_cutoff": 0.01,
"nan_to_num": True,
}
self.data = ScanpyEngine("example-dataset/pbmc3k.h5ad", args)
self.data._create_schema()
@@ -23,8 +28,8 @@ class UtilTest(unittest.TestCase):
def test_init(self):
self.assertEqual(self.data.cell_count, 2638)
self.assertEqual(self.data.gene_count, 1838)
epsilon = 0.000005
self.assertTrue(self.data.data.X[0, 0] - -0.17146951 < epsilon)
epsilon = 0.000_005
self.assertTrue(self.data.data.X[0, 0] - -0.171_469_51 < epsilon)
def test_mandatory_annotations(self):
self.assertIn("name", self.data.data.obs)
@@ -39,69 +44,36 @@ class UtilTest(unittest.TestCase):
self.data._validate_data_types()
def test_filter_idx(self):
filter_ = {
"filter": {
"var": {
"index": [1, 99, [200, 300]]
},
"obs": {
"index": [1, 99, [1000, 2000]]
}
}
}
filter_ = {"filter": {"var": {"index": [1, 99, [200, 300]]}, "obs": {"index": [1, 99, [1000, 2000]]}}}
data = self.data.filter_dataframe(filter_["filter"])
self.assertEqual(data.shape, (1002, 102))
def test_filter_annotation(self):
filter_ = {
"filter": {
"obs": {
"annotation_value": [
{"name": "louvain", "values": ["NK cells", "CD8 T cells"]},
]
}
}
"filter": {"obs": {"annotation_value": [{"name": "louvain", "values": ["NK cells", "CD8 T cells"]}]}}
}
data = self.data.filter_dataframe(filter_["filter"])
self.assertEqual(data.shape, (470, 1838))
filter_ = {
"filter": {
"obs": {
"annotation_value": [
{"name": "n_counts", "min": 3000},
]
}
}
}
filter_ = {"filter": {"obs": {"annotation_value": [{"name": "n_counts", "min": 3000}]}}}
data = self.data.filter_dataframe(filter_["filter"])
self.assertEqual(data.shape, (497, 1838))
def test_filter_annotation_no_uns(self):
filter_ = {
"filter": {
"var": {
"annotation_value": [
{"name": "name", "values": ["RER1"]},
]
}
}
}
filter_ = {"filter": {"var": {"annotation_value": [{"name": "name", "values": ["RER1"]}]}}}
data = self.data.filter_dataframe(filter_["filter"])
self.assertEqual(data.shape[1], 1)
def test_filter_complex(self):
filter_ = {
"filter": {
"var": {
"index": [1, 99, [200, 300]]
},
"var": {"index": [1, 99, [200, 300]]},
"obs": {
"annotation_value": [
{"name": "louvain", "values": ["NK cells", "CD8 T cells"]},
{"name": "n_counts", "min": 3000},
],
"index": [1, 99, [1000, 2000]]
}
"index": [1, 99, [1000, 2000]],
},
}
}
data = self.data.filter_dataframe(filter_["filter"])
@@ -117,13 +89,14 @@ class UtilTest(unittest.TestCase):
self.assertEqual(self.data.schema, schema)
def test_schema_produces_error(self):
self.data.data.obs["time"] = Series(list([time.time() for i in range(self.data.cell_count)]),
dtype="datetime64[ns]")
self.data.data.obs["time"] = Series(
list([time.time() for i in range(self.data.cell_count)]), dtype="datetime64[ns]"
)
with pytest.raises(TypeError):
self.data._create_schema()
def test_config(self):
self.assertEqual(self.data.features["layout"]["obs"], {'available': True, 'interactiveLimit': 50000})
self.assertEqual(self.data.features["layout"]["obs"], {"available": True, "interactiveLimit": 50000})
def test_layout(self):
layout = self.data.layout(None)
@@ -153,16 +126,8 @@ class UtilTest(unittest.TestCase):
def test_filtered_annotation(self):
filter_ = {
"filter": {
"obs": {
"annotation_value": [
{"name": "n_counts", "min": 3000},
]
},
"var": {
"annotation_value": [
{"name": "name", "values": ["ATAD3C", "RER1"]},
]
}
"obs": {"annotation_value": [{"name": "n_counts", "min": 3000}]},
"var": {"annotation_value": [{"name": "name", "values": ["ATAD3C", "RER1"]}]},
}
}
annotations = self.data.annotation(filter_["filter"], "obs")
@@ -173,33 +138,13 @@ class UtilTest(unittest.TestCase):
self.assertEqual(len(annotations["data"]), 2)
def test_filtered_layout(self):
filter_ = {
"filter": {
"obs": {
"annotation_value": [
{"name": "n_counts", "min": 3000},
]
}
}
}
filter_ = {"filter": {"obs": {"annotation_value": [{"name": "n_counts", "min": 3000}]}}}
layout = self.data.layout(filter_["filter"])
self.assertEqual(len(layout["coordinates"]), 497)
def test_diffexp_topN(self):
f1 = {
"filter": {
"obs": {
"index": [[0, 500]]
}
}
}
f2 = {
"filter": {
"obs": {
"index": [[500, 1000]]
}
}
}
f1 = {"filter": {"obs": {"index": [[0, 500]]}}}
f2 = {"filter": {"obs": {"index": [[500, 1000]]}}}
result = self.data.diffexp_topN(f1["filter"], f2["filter"])
self.assertEqual(len(result), 10)
result = self.data.diffexp_topN(f1["filter"], f2["filter"], 20)
@@ -214,15 +159,7 @@ class UtilTest(unittest.TestCase):
self.assertEqual(len(data_frame_var["obs"]), 2638)
def test_filtered_data_frame(self):
filter_ = {
"filter": {
"obs": {
"annotation_value": [
{"name": "n_counts", "min": 3000},
]
}
}
}
filter_ = {"filter": {"obs": {"annotation_value": [{"name": "n_counts", "min": 3000}]}}}
data_frame_obs = self.data.data_frame(filter_["filter"], "obs")
self.assertEqual(len(data_frame_obs["var"]), 1838)
self.assertEqual(len(data_frame_obs["obs"]), 497)
@@ -236,15 +173,7 @@ class UtilTest(unittest.TestCase):
def test_data_single_gene(self):
for axis in ["obs", "var"]:
filter_ = {
"filter": {
"var": {
"annotation_value": [
{"name": "name", "values": ["RER1"]},
]
}
}
}
filter_ = {"filter": {"var": {"annotation_value": [{"name": "name", "values": ["RER1"]}]}}}
data_frame_var = self.data.data_frame(filter_["filter"], axis)
if axis == "obs":
self.assertEqual(type(data_frame_var["var"][0]), int)
@@ -253,5 +182,5 @@ class UtilTest(unittest.TestCase):
self.assertEqual(type(data_frame_var["obs"][0]), int)
self.assertIsInstance(data_frame_var["var"][0], (list, tuple))
if __name__ == '__main__':
if __name__ == "__main__":
unittest.main()