From 76c1d9e80cbb7df4236b72c66324e3bdd6dc7791 Mon Sep 17 00:00:00 2001
From: Alok Saldanha <aloksaldanha@gmail.com>
Date: Mon, 29 Mar 2021 07:28:16 -0400
Subject: [PATCH] removed .csv suffix from annotation name

---
 cellxgene_gateway/items/file/fileitem.py      |  5 +++--
 .../items/file/fileitem_source.py             |  9 ++++++++-
 tests/items/__init__.py                       |  0
 tests/items/file/__init__.py                  |  0
 tests/items/file/test_fileitem_source.py      | 20 +++++++++++++++++++
 tests/test_cache_entry.py                     |  2 +-
 6 files changed, 32 insertions(+), 4 deletions(-)
 create mode 100644 tests/items/__init__.py
 create mode 100644 tests/items/file/__init__.py
 create mode 100644 tests/items/file/test_fileitem_source.py

diff --git a/cellxgene_gateway/items/file/fileitem.py b/cellxgene_gateway/items/file/fileitem.py
index 5951b2e..cd5c011 100644
--- a/cellxgene_gateway/items/file/fileitem.py
+++ b/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("/")
diff --git a/cellxgene_gateway/items/file/fileitem_source.py b/cellxgene_gateway/items/file/fileitem_source.py
index 073425c..5a23048 100644
--- a/cellxgene_gateway/items/file/fileitem_source.py
+++ b/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,
         )
 
diff --git a/tests/items/__init__.py b/tests/items/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/tests/items/file/__init__.py b/tests/items/file/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/tests/items/file/test_fileitem_source.py b/tests/items/file/test_fileitem_source.py
new file mode 100644
index 0000000..9350690
--- /dev/null
+++ b/tests/items/file/test_fileitem_source.py
@@ -0,0 +1,20 @@
+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")
diff --git a/tests/test_cache_entry.py b/tests/test_cache_entry.py
index 7f076c9..6ad04bd 100644
--- a/tests/test_cache_entry.py
+++ b/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"),
 )