#78 Revert "Rename argument "filter" to "subpath""

This reverts commit fdd6cca297.

cellxgene_gateway/cache_entry.py

@@ -58,7 +58,6 @@ class CacheEntry:
 
     @classmethod
     def for_key(cls, key, port):
-
         return cls(
             None,
             key,

cellxgene_gateway/filecrawl.py

@@ -60,8 +60,8 @@ def render_item_tree(item_tree, item_source):
         return html
 
 
-def render_item_source(item_source, path=None):
+def render_item_source(item_source, filter=None):
-    item_tree = item_source.list_items(path)
+    item_tree = item_source.list_items(filter)
-    path_part = "" if path is None else ":" + path
+    filterpart = "" if filter is None else ":" + filter
-    heading = f"<h6><a href='/filecrawl.html?source={urllib.parse.quote_plus(item_source.name)}'>{item_source.name}</a>{path_part}</h6>"
+    heading = f"<h6><a href='/filecrawl.html?source={urllib.parse.quote_plus(item_source.name)}'>{item_source.name}</a>{filterpart}</h6>"
     return heading + render_item_tree(item_tree, item_source)

cellxgene_gateway/gateway.py

@@ -80,7 +80,6 @@ cache = BackendCache()
 
 @app.errorhandler(CellxgeneException)
 def handle_invalid_usage(error):
-
     message = f"{error.http_status} Error : {error.message}"
 
     return (
@@ -95,7 +94,6 @@ def handle_invalid_usage(error):
 
 @app.errorhandler(ProcessException)
 def handle_invalid_process(error):
-
     message = []
 
     message.append(error.message)

cellxgene_gateway/items/file/fileitem_source.py

@@ -50,8 +50,8 @@ class FileItemSource(ItemSource):
     def get_annotations_subpath(self, item) -> str:
         return self.convert_h5ad_path_to_annotation(item.descriptor)
 
-    def list_items(self, subpath: str = None) -> ItemTree:
+    def list_items(self, filter: str = None) -> ItemTree:
-        item_tree = self.scan_directory("" if subpath is None else subpath)
+        item_tree = self.scan_directory("" if filter is None else filter)
 
         """def get_items(dir):
             if dir.branches:
@@ -102,7 +102,9 @@ class FileItemSource(ItemSource):
             ]
             # Exclude branches without files as leaves. Since traversal is applied pre-order,
             # branch.branches has already been processed and we don't need to check deeper nesting.
-            branches = [branch for branch in branches if branch.items or branch.branches]
+            branches = [
+                branch for branch in branches if branch.items or branch.branches
+            ]
 
         return ItemTree(subpath, items, branches)
 

cellxgene_gateway/items/item_source.py

@@ -21,7 +21,7 @@ class LookupResult:
 
 class ItemSource(ABC):
     @abstractmethod
-    def list_items(self, subpath: str = None) -> List[Item]:
+    def list_items(self, filter: str = None) -> List[Item]:
         raise Exception('"list_items" unimplemented')
 
     @abstractmethod

cellxgene_gateway/items/s3/s3item_source.py

@@ -72,8 +72,8 @@ class S3ItemSource(ItemSource):
     def get_annotations_subpath(self, item) -> str:
         return self.convert_h5ad_key_to_annotation(item.descriptor)
 
-    def list_items(self, subpath: str = None) -> ItemTree:
+    def list_items(self, filter: str = None) -> ItemTree:
-        item_tree = self.scan_directory("" if subpath is None else subpath)
+        item_tree = self.scan_directory("" if filter is None else filter)
         return item_tree
 
     @property
@@ -116,7 +116,9 @@ class S3ItemSource(ItemSource):
         branches = None
         if len(subdir_keys) > 0:
             branches = [self.scan_directory(key) for key in subdir_keys]
-            branches = [branch for branch in branches if branch.items or branch.branches]
+            branches = [
+                branch for branch in branches if branch.items or branch.branches
+            ]
 
         return ItemTree(directory_key, items, branches)
 

tests/test_filecrawl.py

@@ -51,6 +51,7 @@ class TestRenderItemSource(unittest.TestCase):
 class TestRenderItemTree(unittest.TestCase):
     def setUp(self):
         from cellxgene_gateway.gateway import app
+
         self.app = app
         self.app_context = self.app.test_request_context()
         self.app_context.push()
@@ -72,9 +73,16 @@ class TestRenderItemTree(unittest.TestCase):
             "</li></ul></li>",
         )
 
-    @patch("os.listdir", side_effect=lambda parent: defaultdict(list, {"tmp": ["foo"], "tmp/foo": ["bar"]})[parent])
+    @patch(
+        "os.listdir",
+        side_effect=lambda parent: defaultdict(
+            list, {"tmp": ["foo"], "tmp/foo": ["bar"]}
+        )[parent],
+    )
     @patch("os.path.exists", return_value=True)
-    def test_GIVEN_dirs_without_h5ad_THEN_excludes_dirs_in_output(self, listdir, exists):
+    def test_GIVEN_dirs_without_h5ad_THEN_excludes_dirs_in_output(
+        self, listdir, exists
+    ):
         # Directories:
         # - tmp
         #   - foo