From fdd6cca29704a13ff8c9cd17e98971c999e0a91d Mon Sep 17 00:00:00 2001
From: Andreas Eisenbarth <andreas.eisenbarth@embl.de>
Date: Wed, 12 Oct 2022 13:40:39 +0200
Subject: [PATCH] Rename argument "filter" to "subpath"

---
 cellxgene_gateway/filecrawl.py                  | 8 ++++----
 cellxgene_gateway/items/file/fileitem_source.py | 4 ++--
 cellxgene_gateway/items/item_source.py          | 2 +-
 cellxgene_gateway/items/s3/s3item_source.py     | 4 ++--
 4 files changed, 9 insertions(+), 9 deletions(-)

diff --git a/cellxgene_gateway/filecrawl.py b/cellxgene_gateway/filecrawl.py
index f812091..2ae9487 100644
--- a/cellxgene_gateway/filecrawl.py
+++ b/cellxgene_gateway/filecrawl.py
@@ -60,8 +60,8 @@ def render_item_tree(item_tree, item_source):
         return html
 
 
-def render_item_source(item_source, filter=None):
-    item_tree = item_source.list_items(filter)
-    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>{filterpart}</h6>"
+def render_item_source(item_source, path=None):
+    item_tree = item_source.list_items(path)
+    path_part = "" if path is None else ":" + path
+    heading = f"<h6><a href='/filecrawl.html?source={urllib.parse.quote_plus(item_source.name)}'>{item_source.name}</a>{path_part}</h6>"
     return heading + render_item_tree(item_tree, item_source)
diff --git a/cellxgene_gateway/items/file/fileitem_source.py b/cellxgene_gateway/items/file/fileitem_source.py
index 4ade4b9..22f6ce4 100644
--- a/cellxgene_gateway/items/file/fileitem_source.py
+++ b/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, filter: str = None) -> ItemTree:
-        item_tree = self.scan_directory("" if filter is None else filter)
+    def list_items(self, subpath: str = None) -> ItemTree:
+        item_tree = self.scan_directory("" if subpath is None else subpath)
 
         """def get_items(dir):
             if dir.branches:
diff --git a/cellxgene_gateway/items/item_source.py b/cellxgene_gateway/items/item_source.py
index eb778ff..fbc26cc 100644
--- a/cellxgene_gateway/items/item_source.py
+++ b/cellxgene_gateway/items/item_source.py
@@ -21,7 +21,7 @@ class LookupResult:
 
 class ItemSource(ABC):
     @abstractmethod
-    def list_items(self, filter: str = None) -> List[Item]:
+    def list_items(self, subpath: str = None) -> List[Item]:
         raise Exception('"list_items" unimplemented')
 
     @abstractmethod
diff --git a/cellxgene_gateway/items/s3/s3item_source.py b/cellxgene_gateway/items/s3/s3item_source.py
index 130df19..a98fc16 100644
--- a/cellxgene_gateway/items/s3/s3item_source.py
+++ b/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, filter: str = None) -> ItemTree:
-        item_tree = self.scan_directory("" if filter is None else filter)
+    def list_items(self, subpath: str = None) -> ItemTree:
+        item_tree = self.scan_directory("" if subpath is None else subpath)
         return item_tree
 
     @property