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cellxgene/server/test/test_api.py
Bruce Martin 00a68276a2 diffexp performance & UX improvements (#431) 
* new diffexp REST API spec

* new diffexp REST API; faster diffexp and dataframe slicing

* first draft of fast diffexp

* convert variance calculation to two-pass method

* lint

* update front-end use of API

* fix typo in spec

* disable content compression

* catch index filter format errors

* clean up of dead code

* resolve PR review comments
2018-11-14 12:51:24 -08:00

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from http import HTTPStatus
from subprocess import Popen
import unittest
import time
import requests
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"},
],
}
}
}
class EndPoints(unittest.TestCase):
"""Test Case for endpoints"""
@classmethod
def setUpClass(cls):
cls.ps = Popen(["cellxgene", "launch", "example-dataset/pbmc3k.h5ad", "--debug"])
session = requests.Session()
for i in range(90):
try:
session.get(f"{URL_BASE}schema")
except requests.exceptions.ConnectionError:
time.sleep(1)
@classmethod
def tearDownClass(cls):
try:
cls.ps.terminate()
except ProcessLookupError:
pass
def setUp(self):
self.session = requests.Session()
def test_initialize(self):
endpoint = "schema"
url = f"{URL_BASE}{endpoint}"
result = self.session.get(url)
self.assertEqual(result.status_code, HTTPStatus.OK)
result_data = result.json()
self.assertEqual(result_data["schema"]["dataframe"]["nObs"], 2638)
self.assertEqual(len(result_data["schema"]["annotations"]["obs"]), 5)
def test_config(self):
endpoint = "config"
url = f"{URL_BASE}{endpoint}"
result = self.session.get(url)
self.assertEqual(result.status_code, HTTPStatus.OK)
result_data = result.json()
self.assertEqual(result_data["config"]["displayNames"]["dataset"], "pbmc3k")
self.assertEqual(len(result_data["config"]["features"]), 4)
def test_get_layout(self):
endpoint = "layout/obs"
url = f"{URL_BASE}{endpoint}"
result = self.session.get(url)
self.assertEqual(result.status_code, HTTPStatus.OK)
result_data = result.json()
self.assertEqual(result_data["layout"]["ndims"], 2)
self.assertEqual(len(result_data["layout"]["coordinates"]), 2638)
# def test_put_layout(self):
# endpoint = "layout/obs"
# url = f"{URL_BASE}{endpoint}"
# obs_filter = {
# "filter": {
# "obs": {
# "annotation_value": [
# {"name": "louvain", "values": ["NK cells", "CD8 T cells"]},
# {"name": "n_counts", "min": 3000},
# ],
# "index": [1, 99, [1000, 2000]]
# }
# }
# }
# result = self.session.put(url, json=obs_filter)
# self.assertEqual(result.status_code, HTTPStatus.OK)
# result_data = result.json()
# self.assertEqual(len(result_data["layout"]["coordinates"]), 15)
def test_bad_filter(self):
endpoints = ["annotations/obs", "annotations/var", "data/obs", "data/var"]
for endpoint in endpoints:
url = f"{URL_BASE}{endpoint}"
result = self.session.put(url, json=BAD_FILTER)
self.assertEqual(result.status_code, HTTPStatus.BAD_REQUEST)
def test_get_annotations_obs(self):
endpoint = "annotations/obs"
url = f"{URL_BASE}{endpoint}"
result = self.session.get(url)
self.assertEqual(result.status_code, HTTPStatus.OK)
result_data = result.json()
self.assertEqual(result_data["names"], ["name", "n_genes", "percent_mito", "n_counts", "louvain"])
self.assertEqual(len(result_data["data"]), 2638)
self.assertEqual(len(result_data["data"][0]), 6)
def test_get_annotations_obs_keys(self):
endpoint = "annotations/obs"
query = "annotation-name=n_genes&annotation-name=percent_mito"
url = f"{URL_BASE}{endpoint}?{query}"
result = self.session.get(url)
self.assertEqual(result.status_code, HTTPStatus.OK)
result_data = result.json()
self.assertEqual(result_data["names"], ["n_genes", "percent_mito"])
self.assertEqual(len(result_data["data"][0]), 3)
def test_get_annotations_obs_error(self):
endpoint = "annotations/obs"
query = "annotation-name=notakey"
url = f"{URL_BASE}{endpoint}?{query}"
result = self.session.get(url)
self.assertEqual(result.status_code, HTTPStatus.BAD_REQUEST)
def test_put_annotations_obs(self):
endpoint = "annotations/obs"
url = f"{URL_BASE}{endpoint}"
obs_filter = {
"filter": {
"obs": {
"annotation_value": [
{"name": "louvain", "values": ["NK cells", "CD8 T cells"]},
{"name": "n_counts", "min": 3000},
],
"index": [1, 99, [1000, 2000]]
}
}
}
result = self.session.put(url, json=obs_filter)
self.assertEqual(result.status_code, HTTPStatus.OK)
result_data = result.json()
self.assertEqual(result_data["names"], ["name", "n_genes", "percent_mito", "n_counts", "louvain"])
self.assertEqual(len(result_data["data"]), 15)
def test_filter_put_annotations_obs(self):
endpoint = "annotations/obs"
query = "annotation-name=n_genes&annotation-name=percent_mito"
url = f"{URL_BASE}{endpoint}?{query}"
obs_filter = {
"filter": {
"obs": {
"annotation_value": [
{"name": "louvain", "values": ["NK cells", "CD8 T cells"]},
{"name": "n_counts", "min": 3000},
],
"index": [1, 99, [1000, 2000]]
}
}
}
result = self.session.put(url, json=obs_filter)
self.assertEqual(result.status_code, HTTPStatus.OK)
result_data = result.json()
self.assertEqual(result_data["names"], ["n_genes", "percent_mito"])
self.assertEqual(len(result_data["data"][0]), 3)
self.assertEqual(len(result_data["data"]), 15)
def test_diff_exp(self):
endpoint = "diffexp/obs"
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
}
result = self.session.post(url, json=params)
self.assertEqual(result.status_code, HTTPStatus.OK)
result_data = result.json()
self.assertEqual(len(result_data), 7)
def test_diff_exp_indices(self):
endpoint = "diffexp/obs"
url = f"{URL_BASE}{endpoint}"
params = {
"mode": "topN",
"count": 10,
"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)
result_data = result.json()
self.assertEqual(len(result_data), 10)
def test_get_annotations_var(self):
endpoint = "annotations/var"
url = f"{URL_BASE}{endpoint}"
result = self.session.get(url)
self.assertEqual(result.status_code, HTTPStatus.OK)
result_data = result.json()
self.assertEqual(result_data["names"], ["name", "n_cells"])
self.assertEqual(len(result_data["data"]), 1838)
self.assertEqual(len(result_data["data"][0]), 3)
def test_get_annotations_var_keys(self):
endpoint = "annotations/var"
query = "annotation-name=n_cells"
url = f"{URL_BASE}{endpoint}?{query}"
result = self.session.get(url)
self.assertEqual(result.status_code, HTTPStatus.OK)
result_data = result.json()
self.assertEqual(result_data["names"], ["n_cells"])
self.assertEqual(len(result_data["data"][0]), 2)
def test_get_annotations_var_error(self):
endpoint = "annotations/var"
query = "annotation-name=notakey"
url = f"{URL_BASE}{endpoint}?{query}"
result = self.session.get(url)
self.assertEqual(result.status_code, HTTPStatus.BAD_REQUEST)
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"]},
]
}
}
}
result = self.session.put(url, json=var_filter)
self.assertEqual(result.status_code, HTTPStatus.OK)
result_data = result.json()
self.assertEqual(result_data["names"], ["name", "n_cells"])
self.assertEqual(len(result_data["data"]), 2)
def test_filter_put_annotations_var(self):
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"]},
]
}
}
}
result = self.session.put(url, json=var_filter)
self.assertEqual(result.status_code, HTTPStatus.OK)
result_data = result.json()
self.assertEqual(result_data["names"], ["n_cells"])
self.assertEqual(len(result_data["data"][0]), 2)
self.assertEqual(len(result_data["data"]), 2)
def test_get_data(self):
for axis in ["obs", "var"]:
endpoint = f"data/{axis}"
query = "accept-type=application/json"
url = f"{URL_BASE}{endpoint}?{query}"
result = self.session.get(url)
self.assertEqual(result.status_code, HTTPStatus.OK)
result_data = result.json()
self.assertEqual(len(result_data["obs"]), 2638)
def test_data_mimetype_error(self):
for axis in ["obs", "var"]:
endpoint = f"data/{axis}"
query = "accept-type=xxx"
url = f"{URL_BASE}{endpoint}?{query}"
result = self.session.get(url)
self.assertEqual(result.status_code, HTTPStatus.NOT_ACCEPTABLE)
url = f"{URL_BASE}{endpoint}"
header = {"Accept": "sdkljfa;dsjalkj"}
result = self.session.get(url, headers=header)
self.assertEqual(result.status_code, HTTPStatus.NOT_ACCEPTABLE)
def test_json_default(self):
for axis in ["obs", "var"]:
endpoint = f"data/{axis}"
url = f"{URL_BASE}{endpoint}"
result = self.session.get(url)
self.assertEqual(result.status_code, HTTPStatus.OK)
def test_data_filter(self):
for axis in ["obs", "var"]:
endpoint = f"data/{axis}"
query = "accept-type=application/json&obs:louvain=NK cells&obs:louvain=CD8 T cells&obs:n_counts=3000,*"
url = f"{URL_BASE}{endpoint}?{query}"
result = self.session.get(url)
self.assertEqual(result.status_code, HTTPStatus.OK)
result_data = result.json()
self.assertEqual(len(result_data["obs"]), 38)
def test_data_put(self):
for axis in ["obs", "var"]:
endpoint = f"data/{axis}"
url = f"{URL_BASE}{endpoint}"
header = {"Accept": "application/json"}
obs_filter = {
"filter": {
"obs": {
"annotation_value": [
{"name": "louvain", "values": ["NK cells", "CD8 T cells"]},
{"name": "n_counts", "min": 3000},
],
"index": [1, 99, [1000, 2000]]
}
}
}
result = self.session.put(url, headers=header, json=obs_filter)
self.assertEqual(result.status_code, HTTPStatus.OK)
result_data = result.json()
self.assertEqual(len(result_data["obs"]), 15)
def test_data_put_single_var(self):
for axis in ["obs", "var"]:
endpoint = f"data/{axis}"
url = f"{URL_BASE}{endpoint}"
header = {"Accept": "application/json"}
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()
if axis == "obs":
self.assertEqual(len(result_data["obs"][0]), 2)
self.assertEqual(len(result_data["var"]), 1)
elif axis == "var":
self.assertEqual(len(result_data["obs"]), 2638)
self.assertEqual(len(result_data["var"][0]), 2639)
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"]}]}}}
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"]}]}}}
result = self.session.put(url, json=f2)
self.assertEqual(result.status_code, HTTPStatus.OK)
result_data2 = result.json()
self.assertNotEqual(result_data1, result_data2)
def test_cache_nofilter(self):
endpoint = "annotations/var"
url = f"{URL_BASE}{endpoint}"
f1 = {"filter": {}}
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"]}]}}}
result = self.session.put(url, json=f2)
self.assertEqual(result.status_code, HTTPStatus.OK)
result_data2 = result.json()
self.assertNotEqual(result_data1, result_data2)
def test_static(self):
endpoint = "static"
file = "js/service-worker.js"
url = f"{LOCAL_URL}{endpoint}/{file}"
result = self.session.get(url)
self.assertEqual(result.status_code, HTTPStatus.OK)
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