Merge pull request #67 from Novartis/docker

Remove version pins to upgrade Flask

environment.yml

@@ -2,9 +2,9 @@ name: cellxgene-gateway
 channels:
 - conda-forge
 dependencies:
-- python=3.7
+- python=3.9
 - requests
-- flask<2.0.0,>=1.0.2
+- flask
 - psutil
 - black
 - twine
@@ -13,6 +13,6 @@ dependencies:
 - pip
 - pip:
   - pre_commit
-  - flask-api==2.0
+  - flask-api
-  - werkzeug==1.0.1
+  - werkzeug
-  - cellxgene>=0.15
+  - cellxgene

requirements.txt

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

tests/items/s3/test_s3item_source.py

@@ -1,6 +1,7 @@
 import unittest
 from unittest.mock import MagicMock, Mock, patch
 
+from cellxgene_gateway.gateway import app
 from cellxgene_gateway.items.item import ItemType
 from cellxgene_gateway.items.s3.s3item import S3Item
 from cellxgene_gateway.items.s3.s3item_source import S3ItemSource
@@ -24,10 +25,7 @@ class TestScanDirectory(unittest.TestCase):
         )
 
     @patch("s3fs.S3FileSystem")
-    @patch("flask.request")
+    def test__GIVEN_multilevel_bucket_THEN_properly_recurses_suburls(self, s3func):
-    def test__GIVEN_multilevel_bucket_THEN_properly_recurses_suburls(
-        self, requestMock, s3func
-    ):
         class S3Mock:
             def exists(path):
                 if path in [
@@ -83,8 +81,8 @@ class TestScanDirectory(unittest.TestCase):
                 raise Exception("isfile called with " + path)
 
         s3func.return_value = S3Mock
-        requestMock.args.get.return_value = "true"
         source = S3ItemSource("my-bucket")
+        with app.test_request_context(query_string="refresh=true") as test_context:
             tree = source.scan_directory()
 
         def s3item_compare(i1, i2, msg=""):