blackened code

cellxgene_gateway/cache_entry.py

@@ -26,6 +26,7 @@ class CacheEntryStatus(Enum):
     error = "error"
     terminated = "terminated"
 
+
 class CacheEntry:
     def __init__(
         self,

cellxgene_gateway/env.py

@@ -24,15 +24,16 @@ external_protocol = os.environ.get(
 ip = os.environ.get("GATEWAY_IP")
 extra_scripts = os.environ.get("GATEWAY_EXTRA_SCRIPTS")
 ttl = os.environ.get("GATEWAY_TTL")
-enable_upload = os.environ.get(
+enable_upload = os.environ.get("GATEWAY_ENABLE_UPLOAD", "").lower() in [
-    "GATEWAY_ENABLE_UPLOAD", ""
+    "true",
-).lower() in ["true", "1"]
+    "1",
+]
 enable_annotations = os.environ.get(
     "GATEWAY_ENABLE_ANNOTATIONS", ""
 ).lower() in ["true", "1"]
 enable_backed_mode = os.environ.get(
     "GATEWAY_ENABLE_BACKED_MODE", ""
-).lower() in ['true', '1']
+).lower() in ["true", "1"]
 
 env_vars = {
     "CELLXGENE_LOCATION": cellxgene_location,

cellxgene_gateway/filecrawl.py

@@ -9,7 +9,12 @@
 
 import os
 from cellxgene_gateway import env
-from cellxgene_gateway.dir_util import make_h5ad, make_annotations, annotations_suffix
+from cellxgene_gateway.dir_util import (
+    make_h5ad,
+    make_annotations,
+    annotations_suffix,
+)
+
 
 def recurse_dir(path):
     if not os.path.exists(path):
@@ -18,6 +23,7 @@ def recurse_dir(path):
         )
 
     all_entries = sorted(os.listdir(path))
+
     def is_h5ad(el):
         return el.endswith(".h5ad") and os.path.isfile(os.path.join(path, el))
 

cellxgene_gateway/flask_util.py

@@ -9,6 +9,7 @@
 
 from flask import request
 
+
 def querystring():
     qs = request.query_string.decode()
-    return f'?{qs}' if len(qs) > 0 else ''
+    return f"?{qs}" if len(qs) > 0 else ""

cellxgene_gateway/gateway.py

@@ -236,7 +236,10 @@ def do_view(path):
 
     match.timestamp = current_time_stamp()
 
-    if match.status == CacheEntryStatus.loaded or match.status == CacheEntryStatus.loading:
+    if (
+        match.status == CacheEntryStatus.loaded
+        or match.status == CacheEntryStatus.loading
+    ):
         return match.serve_content(path)
     elif match.status == CacheEntryStatus.error:
         raise ProcessException.from_cache_entry(match)

cellxgene_gateway/subprocess_backend.py

@@ -19,7 +19,6 @@ from cellxgene_gateway.path_util import get_annotation_file_path, get_file_path
 from cellxgene_gateway.process_exception import ProcessException
 
 
-
 class SubprocessBackend:
     def __init__(self):
         pass
@@ -29,7 +28,9 @@ class SubprocessBackend:
     ):
         if enable_annotations and not annotation_file_path is None:
             if annotation_file_path == "":
-                extra_args = f" --annotations-dir {make_annotations(file_path)}"
+                extra_args = (
+                    f" --annotations-dir {make_annotations(file_path)}"
+                )
             else:
                 extra_args = f" --annotations-file {annotation_file_path}"
         else:

tests/test_cache_entry.py

@@ -9,5 +9,6 @@ class TestCacheEntry(unittest.TestCase):
         entry = CacheEntry.for_key("some-key", 1)
         self.assertEqual(entry.status, CacheEntryStatus.loading)
 
+
 if __name__ == "__main__":
     unittest.main()

tests/test_filecrawl.py

@@ -10,7 +10,7 @@ class TestRenderEntry(unittest.TestCase):
             "path": "/somepath/",
             "name": "entry",
             "type": "file",
-            "annotations": []
+            "annotations": [],
         }
         rendered = render_entry(entry)
         self.assertIn("view/somepath", rendered)
@@ -20,7 +20,7 @@ class TestRenderEntry(unittest.TestCase):
             "path": "/somepath",
             "name": "entry",
             "type": "file",
-            "annotations": []
+            "annotations": [],
         }
         rendered = render_entry(entry)
         self.assertIn("view/somepath", rendered)
@@ -30,7 +30,7 @@ class TestRenderEntry(unittest.TestCase):
             "path": "somepath/",
             "name": "entry",
             "type": "file",
-            "annotations": []
+            "annotations": [],
         }
         rendered = render_entry(entry)
         self.assertIn("view/somepath", rendered)
@@ -40,7 +40,7 @@ class TestRenderEntry(unittest.TestCase):
             "path": "somepath",
             "name": "entry",
             "type": "file",
-            "annotations": []
+            "annotations": [],
         }
         rendered = render_entry(entry)
         self.assertIn("view/somepath", rendered)