prepare for 0.3.6 release

This is required by earlier flask-api versions

  File "/home/alokito/code/cellxgene-gateway/cellxgene_gateway/gateway.py", line 25, in <module>
    from flask_api import status
  File "/home/alokito/miniconda3/envs/cellxgene-gateway/lib/python3.7/site-packages/flask_api/__init__.py", line 1, in <module>
    from flask_api.app import FlaskAPI
  File "/home/alokito/miniconda3/envs/cellxgene-gateway/lib/python3.7/site-packages/flask_api/app.py", line 6, in <module>
    from flask_api.request import APIRequest
  File "/home/alokito/miniconda3/envs/cellxgene-gateway/lib/python3.7/site-packages/flask_api/request.py", line 9, in <module>
    from werkzeug._compat import to_unicode
ModuleNotFoundError: No module named 'werkzeug._compat'

.pre-commit-config.yaml

@@ -8,7 +8,6 @@ repos:
       types: [python]
       stages: [commit]
     - id: black
-      language_version: python3.6+
       name: black
       language: system
       entry: black

Changelog.md

@@ -1,3 +1,15 @@
+# 0.3.6
+
+* pinned version of werkzeug
+
+# 0.3.5
+
+* Pinned flask version to match cellxgene 0.17.0
+
+# 0.3.4
+
+* Fixed bug #50 affecting subdirectory listing
+
 # 0.3.3
 
 * Fixed bug #48 affecting cache pruning

cellxgene_gateway/__init__.py

@@ -7,4 +7,4 @@
 # OR CONDITIONS OF ANY KIND, either express or implied. See the License for
 # the specific language governing permissions and limitations under the License.
 
-__version__ = "0.3.3"
+__version__ = "0.3.6"

cellxgene_gateway/items/file/fileitem_source.py

@@ -51,7 +51,7 @@ class FileItemSource(ItemSource):
         return self.convert_h5ad_path_to_annotation(item.descriptor)
 
     def list_items(self, filter: str = None) -> ItemTree:
-        item_tree = self.scan_directory()
+        item_tree = self.scan_directory("" if filter is None else filter)
 
         """def get_items(dir):
             if dir.branches:

environment.yml

@@ -4,11 +4,15 @@ channels:
 dependencies:
 - python=3.7
 - requests
-- flask
+- flask<2.0.0,>=1.0.2
 - psutil
 - black
+- twine
+- isort
 - coverage
 - pip
 - pip:
-  - flask-api
+  - pre_commit
+  - flask-api==2.0
+  - werkzeug==1.0.1
   - cellxgene>=0.15

requirements.txt

@@ -1,5 +1,6 @@
 cellxgene>=0.15
-flask
-flask_api
+flask<2.0.0,>=1.0.2
+flask-api==2.0
+werkzeug==1.0.1
 psutil
 requests

tests/items/file/test_fileitem_source.py

@@ -1,10 +1,31 @@
 import tempfile
 import unittest
+from unittest.mock import patch
 
 from cellxgene_gateway.items.file.fileitem_source import FileItemSource
 
 
+def stub_join(path):
+    path.join = lambda x, y: x + "/" + y
+
+
 class TestFileItemSource(unittest.TestCase):
+    @patch("os.path")
+    @patch("os.listdir")
+    def test_list_items_GIVEN_no_subpath_THEN_checks_dir(self, listdir, path):
+        stub_join(path)
+        source = FileItemSource("/tmp/unittest", "local")
+        source.list_items()
+        path.exists.assert_called_once_with("/tmp/unittest/")
+
+    @patch("os.path")
+    @patch("os.listdir")
+    def test_list_items_GIVEN_subpath_THEN_checks_subpath(self, listdir, path):
+        stub_join(path)
+        source = FileItemSource("/tmp/unittest", "local")
+        source.list_items("foo")
+        path.exists.assert_called_once_with("/tmp/unittest/foo")
+
     def test_make_fileitem_from_path_GIVEN_annotation_file_THEN_name_lacks_csv(
         self,
     ):