#66 switched from mocks to test request context

#59 add refresh query param to force refresh of S3 cache

Changelog.md

@@ -1,3 +1,7 @@
+# 0.3.9
+
+* Added S3_ENABLE_LISTINGS_CACHE variable (See README.md)
+
 # 0.3.8
 
 * Fixed bug #57 affecting deeply nested subdirectory listing

Dockerfile

@@ -0,0 +1,8 @@
+FROM python:3.9
+
+RUN pip install cellxgene-gateway 'MarkupSafe<2.1'
+
+ENV CELLXGENE_DATA=/cellxgene-data
+ENV CELLXGENE_LOCATION=/usr/local/bin/cellxgene
+
+CMD ["cellxgene-gateway"]

README.md

@@ -76,7 +76,7 @@ Optional environment variables:
 * `GATEWAY_EXTRA_SCRIPTS` - JSON array of script paths, will be embedded into each page and forwarded with `--scripts` to cellxgene server
 * `GATEWAY_ENABLE_ANNOTATIONS` - Set to `true` or to `1` to enable cellxgene annotations. 
 * `GATEWAY_ENABLE_BACKED_MODE` - Set to `true` or to `1` to load AnnData in file-backed mode. This saves memory and speeds up launch time but may reduce overall performance.
-* `S3_ENABLE_LISTINGS_CACHE` - Set to `true` or to `1` to cache listings of S3 folders for performance. Can be overridden by setting `filecrawl.html?refresh=true` query parameter.
+* `S3_ENABLE_LISTINGS_CACHE` - Set to `true` or to `1` to cache listings of S3 folders for performance. If the cache becomes stale, set `filecrawl.html?refresh=true` query parameter to refresh the cache.
 
 If any of the following optional variables are set, [ProxyFix](https://werkzeug.palletsprojects.com/en/1.0.x/middleware/proxy_fix/) will be used.
 * `PROXY_FIX_FOR` - Number of upstream proxies setting X-Forwarded-For
@@ -87,6 +87,33 @@ If any of the following optional variables are set, [ProxyFix](https://werkzeug.
 
 The defaults should be fine if you set up a venv and cellxgene_data folder as above.
 
+## Running cellxgene-gateway with Docker
+
+First, build Docker image:
+
+```bash
+docker build -t cellxgene-gateway .
+```
+
+Then, cellxgene-gateway can be launched as such:
+
+```bash
+docker run -it --rm \
+-v <local_data_dir>:/cellxgene-data \
+-p 5005:5005 \
+cellxgene-gateway
+```
+
+Additional environment variables can be provided with the `-e` parameter:
+
+```bash
+docker run -it --rm \
+-v <local_data_dir>:/cellxgene-data \
+-e GATEWAY_PORT=8080 \
+-p 8080:8080 \
+cellxgene-gateway
+```
+
 # Customization
 
 The current paradigm for customization is to modify files during a build or deployment phase:

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__ = "0.3.8"
+__version__ = "0.3.9"

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 [
@@ -83,9 +81,9 @@ class TestScanDirectory(unittest.TestCase):
                 raise Exception("isfile called with " + path)
 
         s3func.return_value = S3Mock
-        requestMock.args.get.return_value = "true"
         source = S3ItemSource("my-bucket")
-        tree = source.scan_directory()
+        with app.test_request_context(query_string="refresh=true") as test_context:
+            tree = source.scan_directory()
 
         def s3item_compare(i1, i2, msg=""):
             self.assertEqual(i1.name, i2.name, "name equals")