diff --git a/environment.yml b/environment.yml index 55b3899..2111edc 100644 --- a/environment.yml +++ b/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 - - werkzeug==1.0.1 - - cellxgene>=0.15 + - flask-api + - werkzeug + - cellxgene diff --git a/requirements.txt b/requirements.txt index 3b45a37..f5f698f 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,6 +1,6 @@ -cellxgene>=0.15 -flask<2.0.0,>=1.0.2 -flask-api==2.0 -werkzeug==1.0.1 +cellxgene +flask +flask-api +werkzeug psutil requests diff --git a/tests/items/s3/test_s3item_source.py b/tests/items/s3/test_s3item_source.py index 7dcd124..d96855c 100644 --- a/tests/items/s3/test_s3item_source.py +++ b/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, requestMock, s3func - ): + def test__GIVEN_multilevel_bucket_THEN_properly_recurses_suburls(self, 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")