Move jsonification to engine level (#511)

server/test/test_nan_rest.py

@@ -0,0 +1,96 @@
+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 WithNaNs(unittest.TestCase):
+    """Test Case for endpoints"""
+
+    @classmethod
+    def setUpClass(cls):
+        cls.ps = Popen(
+            ["cellxgene", "launch", "server/test/test_datasets/nan.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)
+
+    def test_errors(self):
+        endpoints = ["annotations/obs", "annotations/var", "data/obs", "data/var"]
+        for endpoint in endpoints:
+            url = f"{URL_BASE}{endpoint}"
+            result = self.session.get(url)
+            self.assertEqual(result.status_code, HTTPStatus.INTERNAL_SERVER_ERROR)
+
+
+class WithoutNaNs(unittest.TestCase):
+    """Test Case for endpoints"""
+
+    @classmethod
+    def setUpClass(cls):
+        cls.ps = Popen(
+            [
+                "cellxgene",
+                "launch",
+                "server/test/test_datasets/nan.h5ad",
+                "--nan-to-num",
+                "--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)
+
+    def test_errors(self):
+        endpoints = ["annotations/obs", "annotations/var", "data/obs", "data/var"]
+        for endpoint in endpoints:
+            url = f"{URL_BASE}{endpoint}"
+            result = self.session.get(url)
+            self.assertEqual(result.status_code, HTTPStatus.OK)