fixed linting and tests

cellxgene_gateway/cache_entry.py

@@ -168,9 +168,8 @@ class CacheEntry:
                 headers[h] = request.headers[h]
 
         full_path = self.cellxgene_basepath() + subpath + querystring()
-
+        cellxgene_response = None
         try:
-            cellxgene_response = None
             if request.method in ["GET", "HEAD", "OPTIONS"]:
                 cellxgene_response = get(full_path, headers=headers)
             elif request.method == "PUT":

cellxgene_gateway/gateway.py

@@ -332,11 +332,13 @@ def launch():
     app.launchtime = current_time_stamp()
     app.run(host="0.0.0.0", port=env.gateway_port, debug=False)
 
+
 # When using servers like Gunicorn or uWSGI, this file is imported rather than run directly.
 # As a result, the main() function is never called automatically.
 # Therefore, we must initialize the data sources at import time to ensure they are available.
 initialize_data_sources()
 
+
 def main():
     """CLI entry point for Flask development server."""
     launch()

tests/items/s3/test_s3item_source.py

@@ -1,13 +1,32 @@
 import unittest
+import os
+import shutil
+import tempfile
+
 from unittest.mock import MagicMock, Mock, patch
 
-from cellxgene_gateway.gateway import app
 from cellxgene_gateway.items.item import ItemType
 from cellxgene_gateway.items.s3.s3item import S3Item
 from cellxgene_gateway.items.s3.s3item_source import S3ItemSource
 
 
 class TestScanDirectory(unittest.TestCase):
+    def setUp(self):
+        self._tmpdir = tempfile.mkdtemp()
+        self._cellxgene_data = os.environ.get("CELLXGENE_DATA", "")
+        os.environ["CELLXGENE_DATA"] = self._tmpdir
+
+        from cellxgene_gateway.gateway import app
+
+        self.app = app
+
+    def tearDown(self):
+        if self._cellxgene_data:
+            os.environ["CELLXGENE_DATA"] = self._cellxgene_data
+        else:
+            del os.environ["CELLXGENE_DATA"]
+        shutil.rmtree(self._tmpdir)
+
     @patch("s3fs.S3FileSystem")
     def test_GIVEN_invalid_bucket_THEN_throws_error(self, s3func):
         class S3Mock:
@@ -26,6 +45,7 @@ class TestScanDirectory(unittest.TestCase):
 
     @patch("s3fs.S3FileSystem")
     def test__GIVEN_multilevel_bucket_THEN_properly_recurses_suburls(self, s3func):
+
         class S3Mock:
             def exists(path):
                 if path in [
@@ -82,7 +102,7 @@ class TestScanDirectory(unittest.TestCase):
 
         s3func.return_value = S3Mock
         source = S3ItemSource("my-bucket")
-        with app.test_request_context(query_string="refresh=true") as test_context:
+        with self.app.test_request_context(query_string="refresh=true") as test_context:
             tree = source.scan_directory()
 
         def s3item_compare(i1, i2, msg=""):

tests/test_cache_entry.py

@@ -1,14 +1,15 @@
 import unittest
+import tempfile
+import os
+import shutil
 
 from flask import Flask
-
 from cellxgene_gateway import flask_util
 from cellxgene_gateway.cache_entry import CacheEntry, CacheEntryStatus
 from cellxgene_gateway.cache_key import CacheKey
-from cellxgene_gateway.gateway import app
+from cellxgene_gateway.items.item import ItemType
 from cellxgene_gateway.items.file.fileitem import FileItem
 from cellxgene_gateway.items.file.fileitem_source import FileItemSource
-from cellxgene_gateway.items.item import ItemType
 
 key = CacheKey(
     FileItem("/czi/", name="pbmc3k.h5ad", type=ItemType.h5ad),
@@ -18,11 +19,25 @@ key = CacheKey(
 
 class TestRenderEntry(unittest.TestCase):
     def setUp(self):
+        self._tmpdir = tempfile.mkdtemp()
+        self._cellxgene_data = os.environ.get("CELLXGENE_DATA", "")
+        os.environ["CELLXGENE_DATA"] = self._tmpdir
+
+        from cellxgene_gateway.gateway import app
+
         self.app = app
         self.app_context = self.app.test_request_context()
         self.app_context.push()
         self.client = self.app.test_client()
 
+    def tearDown(self):
+        self.app_context.pop()
+        if self._cellxgene_data:
+            os.environ["CELLXGENE_DATA"] = self._cellxgene_data
+        else:
+            del os.environ["CELLXGENE_DATA"]
+        shutil.rmtree(self._tmpdir)
+
     def test_GIVEN_key_and_port_THEN_returns_loading_CacheEntry(self):
         entry = CacheEntry.for_key("some-key", 1)
         self.assertEqual(entry.status, CacheEntryStatus.loading)

tests/test_filecrawl.py

@@ -1,3 +1,6 @@
+import os
+import shutil
+import tempfile
 import unittest
 from collections import defaultdict
 from unittest.mock import patch
@@ -25,6 +28,25 @@ def make_entry(subpath="somepath", annotations=None):
 
 
 class TestRenderEntry(unittest.TestCase):
+    def setUp(self):
+        self._tmpdir = tempfile.mkdtemp()
+        self._cellxgene_data = os.environ.get("CELLXGENE_DATA", "")
+        os.environ["CELLXGENE_DATA"] = self._tmpdir
+
+        from cellxgene_gateway.gateway import app
+
+        self.app = app
+        self.app_context = self.app.test_request_context()
+        self.app_context.push()
+
+    def tearDown(self):
+        self.app_context.pop()
+        if self._cellxgene_data:
+            os.environ["CELLXGENE_DATA"] = self._cellxgene_data
+        else:
+            del os.environ["CELLXGENE_DATA"]
+        shutil.rmtree(self._tmpdir)
+
     def test_GIVEN_path_both_slash_THEN_view_has_single_slash(self):
         entry = make_entry(subpath="/somepath/")
         rendered = render_item(entry, source)
@@ -47,6 +69,26 @@ class TestRenderEntry(unittest.TestCase):
 
 
 class TestRenderAnnotation(unittest.TestCase):
+
+    def setUp(self):
+        self._tmpdir = tempfile.mkdtemp()
+        self._cellxgene_data = os.environ.get("CELLXGENE_DATA", "")
+        os.environ["CELLXGENE_DATA"] = self._tmpdir
+
+        from cellxgene_gateway.gateway import app
+
+        self.app = app
+        self.app_context = self.app.test_request_context()
+        self.app_context.push()
+
+    def tearDown(self):
+        self.app_context.pop()
+        if self._cellxgene_data:
+            os.environ["CELLXGENE_DATA"] = self._cellxgene_data
+        else:
+            del os.environ["CELLXGENE_DATA"]
+        shutil.rmtree(self._tmpdir)
+
     @patch("cellxgene_gateway.filecrawl.enable_annotations", new=True)
     def test_GIVEN_no_annotation_THEN_new_alone(self):
         entry = make_entry(annotations=None)
@@ -103,12 +145,24 @@ class TestRenderItemSource(unittest.TestCase):
 
 class TestRenderItemTree(unittest.TestCase):
     def setUp(self):
+        self._tmpdir = tempfile.mkdtemp()
+        self._cellxgene_data = os.environ.get("CELLXGENE_DATA", "")
+        os.environ["CELLXGENE_DATA"] = self._tmpdir
+
         from cellxgene_gateway.gateway import app
 
         self.app = app
         self.app_context = self.app.test_request_context()
         self.app_context.push()
 
+    def tearDown(self):
+        self.app_context.pop()
+        if self._cellxgene_data:
+            os.environ["CELLXGENE_DATA"] = self._cellxgene_data
+        else:
+            del os.environ["CELLXGENE_DATA"]
+        shutil.rmtree(self._tmpdir)
+
     @patch("cellxgene_gateway.items.file.fileitem_source.FileItemSource")
     def test_GIVEN_deep_nested_dirs_THEN_includes_dirs_in_output(self, item_source):
         item_source.name = "FakeSource"