removed .csv suffix from annotation name

cellxgene_gateway/items/file/fileitem.py

@@ -18,10 +18,11 @@ class FileItem(Item):
     The Item superclass expects a 'name' and 'type'.
     """
 
-    def __init__(self, subpath: str, *args, **kwargs):
+    def __init__(self, subpath: str, ext: str = "", *args, **kwargs):
         super().__init__(*args, **kwargs)
         self.subpath = subpath
+        self.ext = ext
 
     @property
     def descriptor(self) -> str:
-        return os.path.join(self.subpath, self.name).strip("/")
+        return os.path.join(self.subpath, self.name + self.ext).strip("/")

cellxgene_gateway/items/file/fileitem_source.py

@@ -150,9 +150,16 @@ class FileItemSource(ItemSource):
     def make_fileitem_from_path(
         self, filename, subpath, is_annotation=False, is_shallow=False
     ) -> FileItem:
+        if is_annotation and filename.endswith(self.annotation_file_suffix):
+            name = filename[: -len(self.annotation_file_suffix)]
+            ext = self.annotation_file_suffix
+        else:
+            name = filename
+            ext = ""
         item = FileItem(
             subpath=subpath,
-            name=filename,
+            name=name,
+            ext=ext,
             type=ItemType.annotation if is_annotation else ItemType.h5ad,
         )
 

tests/items/file/test_fileitem_source.py

+import tempfile
+import unittest
+
+from cellxgene_gateway.items.file.fileitem_source import FileItemSource
+
+
+class TestFileItemSource(unittest.TestCase):
+    def test_make_fileitem_from_path_GIVEN_annotation_file_THEN_name_lacks_csv(self):
+        source = FileItemSource(tempfile.gettempdir(), "local")
+        item = source.make_fileitem_from_path(
+            "customanno.csv", "someh5ad_annotations", True
+        )
+        self.assertEqual(item.name, "customanno")
+        self.assertEqual(item.descriptor, "someh5ad_annotations/customanno.csv")
+
+    def test_make_fileitem_from_path_GIVEN_h5ad_file_THEN_returns_name(self):
+        source = FileItemSource(tempfile.gettempdir(), "local")
+        item = source.make_fileitem_from_path("someanalysis.h5ad", "studydir")
+        self.assertEqual(item.name, "someanalysis.h5ad")
+        self.assertEqual(item.descriptor, "studydir/someanalysis.h5ad")

tests/test_cache_entry.py

@@ -10,7 +10,7 @@ from cellxgene_gateway.items.file.fileitem_source import FileItemSource
 from cellxgene_gateway.items.item import ItemType
 
 key = CacheKey(
-    FileItem("/czi/", "pbmc3k.h5ad", ItemType.h5ad),
+    FileItem("/czi/", name="pbmc3k.h5ad", type=ItemType.h5ad),
     FileItemSource("/tmp", "local"),
 )