mirror of
https://github.com/chanzuckerberg/cellxgene.git
synced 2026-09-15 12:47:56 +08:00
f3015cb9df
* Fix Makefile whitespace and .PHONY use
* Fix Makefile filename
* Modularize Makefile into client and server Makefiles
Part of the reason that the Makefile in the root directory is a bit
complicated is that it tries to handle tasks that can be handled
separately in the client and server modules.
This commit pushes some of the make logic specific to each module into
their own makefiles and calls out to those makefiles from that in the
project root.
* Add auto-formatting to client and server modules
One thing that can make linting faster is auto-formatting. This commit
adds the yapf auto-formatting tool to the server module and uses
eslint's "fix" functionality to speed up the linting/formatting process.
* Add yapf for automatic code formatting
* Add a root test target that calls sub-tests
* Apply yapf to python files
* Do not duplicate npm commands, simply pass through
* Update documentation
* Do not shadow reserved word len
* Add general test target
* Fix make call in dev-env
* Use black instead of yapf
* Run flake8 from the root directory
* Revert "Apply yapf to python files"
This reverts commit cdca128a01.
* Apply black to python code
* Resolve lint errors resulting from black format
* Add explanation of server unit tests in dev guidelines
264 lines
11 KiB
Python
264 lines
11 KiB
Python
from http import HTTPStatus
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from subprocess import Popen
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import unittest
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import time
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import requests
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import decode_fbs
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LOCAL_URL = "http://127.0.0.1:5005/"
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VERSION = "v0.2"
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URL_BASE = f"{LOCAL_URL}api/{VERSION}/"
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BAD_FILTER = {"filter": {"obs": {"annotation_value": [{"name": "xyz"}]}}}
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class EndPoints(unittest.TestCase):
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"""Test Case for endpoints"""
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@classmethod
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def setUpClass(cls):
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cls.ps = Popen(["cellxgene", "launch", "../example-dataset/pbmc3k.h5ad", "--verbose", "--port", "5005"])
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session = requests.Session()
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for i in range(90):
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try:
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result = session.get(f"{URL_BASE}schema")
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cls.schema = result.json()
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except requests.exceptions.ConnectionError:
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time.sleep(1)
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@classmethod
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def tearDownClass(cls):
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try:
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cls.ps.terminate()
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except ProcessLookupError:
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pass
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def setUp(self):
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self.session = requests.Session()
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def test_initialize(self):
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endpoint = "schema"
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url = f"{URL_BASE}{endpoint}"
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result = self.session.get(url)
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self.assertEqual(result.status_code, HTTPStatus.OK)
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self.assertEqual(result.headers["Content-Type"], "application/json")
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result_data = result.json()
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self.assertEqual(result_data["schema"]["dataframe"]["nObs"], 2638)
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self.assertEqual(len(result_data["schema"]["annotations"]["obs"]), 2)
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self.assertEqual(len(result_data["schema"]["annotations"]["obs"]["columns"]), 5)
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def test_config(self):
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endpoint = "config"
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url = f"{URL_BASE}{endpoint}"
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result = self.session.get(url)
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self.assertEqual(result.status_code, HTTPStatus.OK)
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self.assertEqual(result.headers["Content-Type"], "application/json")
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result_data = result.json()
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self.assertIn("library_versions", result_data["config"])
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self.assertEqual(result_data["config"]["displayNames"]["dataset"], "pbmc3k")
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self.assertEqual(len(result_data["config"]["features"]), 4)
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def test_get_layout_fbs(self):
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endpoint = "layout/obs"
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url = f"{URL_BASE}{endpoint}"
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header = {"Accept": "application/octet-stream"}
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result = self.session.get(url, headers=header)
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self.assertEqual(result.status_code, HTTPStatus.OK)
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self.assertEqual(result.headers["Content-Type"], "application/octet-stream")
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df = decode_fbs.decode_matrix_FBS(result.content)
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self.assertEqual(df["n_rows"], 2638)
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self.assertEqual(df["n_cols"], 8)
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self.assertIsNotNone(df["columns"])
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self.assertListEqual(
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df["col_idx"],
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["pca_0", "pca_1", "tsne_0", "tsne_1", "umap_0", "umap_1", "draw_graph_fr_0", "draw_graph_fr_1"],
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)
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self.assertIsNone(df["row_idx"])
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self.assertEqual(len(df["columns"]), df["n_cols"])
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def test_bad_filter(self):
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endpoint = "data/var"
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url = f"{URL_BASE}{endpoint}"
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result = self.session.put(url, json=BAD_FILTER)
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self.assertEqual(result.status_code, HTTPStatus.BAD_REQUEST)
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def test_get_annotations_obs_fbs(self):
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endpoint = "annotations/obs"
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url = f"{URL_BASE}{endpoint}"
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header = {"Accept": "application/octet-stream"}
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result = self.session.get(url, headers=header)
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self.assertEqual(result.status_code, HTTPStatus.OK)
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self.assertEqual(result.headers["Content-Type"], "application/octet-stream")
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df = decode_fbs.decode_matrix_FBS(result.content)
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self.assertEqual(df["n_rows"], 2638)
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self.assertEqual(df["n_cols"], 5)
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self.assertIsNotNone(df["columns"])
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self.assertIsNotNone(df["col_idx"])
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self.assertIsNone(df["row_idx"])
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self.assertEqual(len(df["columns"]), df["n_cols"])
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obs_index_col_name = self.schema["schema"]["annotations"]["obs"]["index"]
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self.assertListEqual(df["col_idx"], [obs_index_col_name, "n_genes", "percent_mito", "n_counts", "louvain"])
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def test_get_annotations_obs_keys_fbs(self):
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endpoint = "annotations/obs"
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query = "annotation-name=n_genes&annotation-name=percent_mito"
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url = f"{URL_BASE}{endpoint}?{query}"
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header = {"Accept": "application/octet-stream"}
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result = self.session.get(url, headers=header)
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self.assertEqual(result.status_code, HTTPStatus.OK)
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self.assertEqual(result.headers["Content-Type"], "application/octet-stream")
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df = decode_fbs.decode_matrix_FBS(result.content)
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self.assertEqual(df["n_rows"], 2638)
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self.assertEqual(df["n_cols"], 2)
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self.assertIsNotNone(df["columns"])
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self.assertIsNotNone(df["col_idx"])
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self.assertIsNone(df["row_idx"])
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self.assertEqual(len(df["columns"]), df["n_cols"])
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self.assertListEqual(df["col_idx"], ["n_genes", "percent_mito"])
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def test_get_annotations_obs_error(self):
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endpoint = "annotations/obs"
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query = "annotation-name=notakey"
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url = f"{URL_BASE}{endpoint}?{query}"
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result = self.session.get(url)
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self.assertEqual(result.status_code, HTTPStatus.BAD_REQUEST)
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def test_diff_exp(self):
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endpoint = "diffexp/obs"
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url = f"{URL_BASE}{endpoint}"
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params = {
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"mode": "topN",
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"set1": {"filter": {"obs": {"annotation_value": [{"name": "louvain", "values": ["NK cells"]}]}}},
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"set2": {"filter": {"obs": {"annotation_value": [{"name": "louvain", "values": ["CD8 T cells"]}]}}},
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"count": 7,
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}
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result = self.session.post(url, json=params)
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self.assertEqual(result.status_code, HTTPStatus.OK)
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self.assertEqual(result.headers["Content-Type"], "application/json")
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result_data = result.json()
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self.assertEqual(len(result_data), 7)
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def test_diff_exp_indices(self):
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endpoint = "diffexp/obs"
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url = f"{URL_BASE}{endpoint}"
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params = {
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"mode": "topN",
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"count": 10,
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"set1": {"filter": {"obs": {"index": [[0, 500]]}}},
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"set2": {"filter": {"obs": {"index": [[500, 1000]]}}},
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}
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result = self.session.post(url, json=params)
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self.assertEqual(result.status_code, HTTPStatus.OK)
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self.assertEqual(result.headers["Content-Type"], "application/json")
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result_data = result.json()
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self.assertEqual(len(result_data), 10)
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def test_get_annotations_var_fbs(self):
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endpoint = "annotations/var"
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url = f"{URL_BASE}{endpoint}"
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header = {"Accept": "application/octet-stream"}
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result = self.session.get(url, headers=header)
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self.assertEqual(result.status_code, HTTPStatus.OK)
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self.assertEqual(result.headers["Content-Type"], "application/octet-stream")
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df = decode_fbs.decode_matrix_FBS(result.content)
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self.assertEqual(df["n_rows"], 1838)
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self.assertEqual(df["n_cols"], 2)
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self.assertIsNotNone(df["columns"])
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self.assertIsNotNone(df["col_idx"])
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self.assertIsNone(df["row_idx"])
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self.assertEqual(len(df["columns"]), df["n_cols"])
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var_index_col_name = self.schema["schema"]["annotations"]["var"]["index"]
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self.assertListEqual(df["col_idx"], [var_index_col_name, "n_cells"])
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def test_get_annotations_var_keys_fbs(self):
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endpoint = "annotations/var"
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query = "annotation-name=n_cells"
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url = f"{URL_BASE}{endpoint}?{query}"
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header = {"Accept": "application/octet-stream"}
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result = self.session.get(url, headers=header)
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self.assertEqual(result.status_code, HTTPStatus.OK)
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self.assertEqual(result.headers["Content-Type"], "application/octet-stream")
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df = decode_fbs.decode_matrix_FBS(result.content)
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self.assertEqual(df["n_rows"], 1838)
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self.assertEqual(df["n_cols"], 1)
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self.assertIsNotNone(df["columns"])
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self.assertIsNotNone(df["col_idx"])
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self.assertIsNone(df["row_idx"])
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self.assertEqual(len(df["columns"]), df["n_cols"])
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self.assertListEqual(df["col_idx"], ["n_cells"])
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def test_get_annotations_var_error(self):
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endpoint = "annotations/var"
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query = "annotation-name=notakey"
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url = f"{URL_BASE}{endpoint}?{query}"
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result = self.session.get(url)
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self.assertEqual(result.status_code, HTTPStatus.BAD_REQUEST)
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def test_data_mimetype_error(self):
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endpoint = f"data/var"
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header = {"Accept": "xxx"}
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url = f"{URL_BASE}{endpoint}"
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result = self.session.put(url, headers=header)
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self.assertEqual(result.status_code, HTTPStatus.NOT_ACCEPTABLE)
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def test_fbs_default(self):
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endpoint = f"data/var"
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url = f"{URL_BASE}{endpoint}"
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result = self.session.put(url)
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self.assertEqual(result.status_code, HTTPStatus.OK)
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self.assertEqual(result.headers["Content-Type"], "application/octet-stream")
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def test_data_put_fbs(self):
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endpoint = f"data/var"
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url = f"{URL_BASE}{endpoint}"
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header = {"Accept": "application/octet-stream"}
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result = self.session.put(url, headers=header)
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self.assertEqual(result.status_code, HTTPStatus.OK)
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self.assertEqual(result.headers["Content-Type"], "application/octet-stream")
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df = decode_fbs.decode_matrix_FBS(result.content)
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self.assertEqual(df["n_rows"], 2638)
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self.assertEqual(df["n_cols"], 1838)
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self.assertIsNotNone(df["columns"])
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self.assertListEqual(df["col_idx"].tolist(), [])
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self.assertIsNone(df["row_idx"])
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self.assertEqual(len(df["columns"]), df["n_cols"])
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def test_data_put_filter_fbs(self):
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endpoint = f"data/var"
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url = f"{URL_BASE}{endpoint}"
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header = {"Accept": "application/octet-stream"}
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filter = {"filter": {"var": {"index": [0, 1, 4]}}}
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result = self.session.put(url, headers=header, json=filter)
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self.assertEqual(result.status_code, HTTPStatus.OK)
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self.assertEqual(result.headers["Content-Type"], "application/octet-stream")
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df = decode_fbs.decode_matrix_FBS(result.content)
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self.assertEqual(df["n_rows"], 2638)
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self.assertEqual(df["n_cols"], 3)
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self.assertIsNotNone(df["columns"])
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self.assertIsNotNone(df["col_idx"])
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self.assertIsNone(df["row_idx"])
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self.assertEqual(len(df["columns"]), df["n_cols"])
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self.assertListEqual(df["col_idx"].tolist(), [0, 1, 4])
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def test_data_put_single_var(self):
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endpoint = f"data/var"
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url = f"{URL_BASE}{endpoint}"
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header = {"Accept": "application/octet-stream"}
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index_col_name = self.schema["schema"]["annotations"]["var"]["index"]
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var_filter = {"filter": {"var": {"annotation_value": [{"name": index_col_name, "values": ["RER1"]}]}}}
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result = self.session.put(url, headers=header, json=var_filter)
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self.assertEqual(result.status_code, HTTPStatus.OK)
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self.assertEqual(result.headers["Content-Type"], "application/octet-stream")
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df = decode_fbs.decode_matrix_FBS(result.content)
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self.assertEqual(df["n_rows"], 2638)
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self.assertEqual(df["n_cols"], 1)
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def test_static(self):
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endpoint = "static"
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file = "js/service-worker.js"
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url = f"{LOCAL_URL}{endpoint}/{file}"
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result = self.session.get(url)
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self.assertEqual(result.status_code, HTTPStatus.OK)
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