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authorzsloan2022-01-14 18:22:32 +0000
committerzsloan2022-01-14 18:22:32 +0000
commit68ac19153b128f60b660e11365e5fd4304c95300 (patch)
tree198e03522af43a2d41f3c02cf3785bcfd4635fc4 /wqflask/tests
parentf588ad96ae5045499860fa6e2740e101ad4410d7 (diff)
parent9ab0c3b6cc146e1711f1478242d4198eed720e4c (diff)
downloadgenenetwork2-68ac19153b128f60b660e11365e5fd4304c95300.tar.gz
Merge branch 'testing' of github.com:genenetwork/genenetwork2 into feature/add_rqtl_pairscan
Diffstat (limited to 'wqflask/tests')
-rw-r--r--wqflask/tests/unit/wqflask/api/test_markdown_routes.py (renamed from wqflask/tests/unit/wqflask/test_markdown_routes.py)10
-rw-r--r--wqflask/tests/unit/wqflask/test_resource_manager.py94
-rw-r--r--wqflask/tests/unit/wqflask/wgcna/__init__.py0
-rw-r--r--wqflask/tests/unit/wqflask/wgcna/test_wgcna.py50
4 files changed, 149 insertions, 5 deletions
diff --git a/wqflask/tests/unit/wqflask/test_markdown_routes.py b/wqflask/tests/unit/wqflask/api/test_markdown_routes.py
index 90e0f17c..1c513ac5 100644
--- a/wqflask/tests/unit/wqflask/test_markdown_routes.py
+++ b/wqflask/tests/unit/wqflask/api/test_markdown_routes.py
@@ -1,10 +1,10 @@
-"""Test functions in markdown utils"""
+"""Test functions for wqflask/api/markdown.py"""
import unittest
from unittest import mock
from dataclasses import dataclass
-from wqflask.markdown_routes import render_markdown
+from wqflask.api.markdown import render_markdown
@dataclass
@@ -24,9 +24,9 @@ This is another sub-heading"""
class TestMarkdownRoutesFunctions(unittest.TestCase):
- """Test cases for functions in markdown_routes"""
+ """Test cases for functions in markdown"""
- @mock.patch('wqflask.markdown_routes.requests.get')
+ @mock.patch('wqflask.api.markdown.requests.get')
def test_render_markdown_when_fetching_locally(self, requests_mock):
requests_mock.return_value = MockRequests404()
markdown_content = render_markdown("general/glossary/glossary.md")
@@ -38,7 +38,7 @@ class TestMarkdownRoutesFunctions(unittest.TestCase):
self.assertRegexpMatches(markdown_content,
"Content for general/glossary/glossary.md not available.")
- @mock.patch('wqflask.markdown_routes.requests.get')
+ @mock.patch('wqflask.api.markdown.requests.get')
def test_render_markdown_when_fetching_remotely(self, requests_mock):
requests_mock.return_value = MockRequests200()
markdown_content = render_markdown("general/glossary/glossary.md")
diff --git a/wqflask/tests/unit/wqflask/test_resource_manager.py b/wqflask/tests/unit/wqflask/test_resource_manager.py
new file mode 100644
index 00000000..f4335425
--- /dev/null
+++ b/wqflask/tests/unit/wqflask/test_resource_manager.py
@@ -0,0 +1,94 @@
+"""Test cases for wqflask/resource_manager.py"""
+import json
+import unittest
+
+from unittest import mock
+from gn3.authentication import get_user_membership
+from gn3.authentication import get_highest_user_access_role
+from gn3.authentication import DataRole
+from gn3.authentication import AdminRole
+
+
+class TestGetUserMembership(unittest.TestCase):
+ """Test cases for `get_user_membership`"""
+
+ def setUp(self):
+ conn = mock.MagicMock()
+ conn.hgetall.return_value = {
+ '7fa95d07-0e2d-4bc5-b47c-448fdc1260b2': (
+ '{"name": "editors", '
+ '"admins": ["8ad942fe-490d-453e-bd37-56f252e41604", "rand"], '
+ '"members": ["8ad942fe-490d-453e-bd37-56f252e41603", '
+ '"rand"], '
+ '"changed_timestamp": "Oct 06 2021 06:39PM", '
+ '"created_timestamp": "Oct 06 2021 06:39PM"}')}
+ self.conn = conn
+
+ def test_user_is_group_member_only(self):
+ """Test that a user is only a group member"""
+ self.assertEqual(
+ get_user_membership(
+ conn=self.conn,
+ user_id="8ad942fe-490d-453e-bd37-56f252e41603",
+ group_id="7fa95d07-0e2d-4bc5-b47c-448fdc1260b2"),
+ {"member": True,
+ "admin": False})
+
+ def test_user_is_group_admin_only(self):
+ """Test that a user is a group admin only"""
+ self.assertEqual(
+ get_user_membership(
+ conn=self.conn,
+ user_id="8ad942fe-490d-453e-bd37-56f252e41604",
+ group_id="7fa95d07-0e2d-4bc5-b47c-448fdc1260b2"),
+ {"member": False,
+ "admin": True})
+
+ def test_user_is_both_group_member_and_admin(self):
+ """Test that a user is both an admin and member of a group"""
+ self.assertEqual(
+ get_user_membership(
+ conn=self.conn,
+ user_id="rand",
+ group_id="7fa95d07-0e2d-4bc5-b47c-448fdc1260b2"),
+ {"member": True,
+ "admin": True})
+
+
+class TestCheckUserAccessRole(unittest.TestCase):
+ """Test cases for `get_highest_user_access_role`"""
+
+ @mock.patch("wqflask.resource_manager.requests.get")
+ def test_edit_access(self, requests_mock):
+ """Test that the right access roles are set"""
+ response = mock.PropertyMock(return_value=json.dumps(
+ {
+ 'data': ['no-access', 'view', 'edit', ],
+ 'metadata': ['no-access', 'view', 'edit', ],
+ 'admin': ['not-admin', 'edit-access', ],
+ }
+ ))
+ type(requests_mock.return_value).content = response
+ self.assertEqual(get_highest_user_access_role(
+ resource_id="0196d92e1665091f202f",
+ user_id="8ad942fe-490d-453e-bd37"),
+ {"data": DataRole.EDIT,
+ "metadata": DataRole.EDIT,
+ "admin": AdminRole.EDIT_ACCESS})
+
+ @mock.patch("wqflask.resource_manager.requests.get")
+ def test_no_access(self, requests_mock):
+ response = mock.PropertyMock(return_value=json.dumps(
+ {
+ 'data': ['no-access', ],
+ 'metadata': ['no-access', ],
+ 'admin': ['not-admin', ],
+ }
+ ))
+ type(requests_mock.return_value).content = response
+ self.assertEqual(get_highest_user_access_role(
+ resource_id="0196d92e1665091f202f",
+ user_id=""),
+ {"data": DataRole.NO_ACCESS,
+ "metadata": DataRole.NO_ACCESS,
+ "admin": AdminRole.NOT_ADMIN})
diff --git a/wqflask/tests/unit/wqflask/wgcna/__init__.py b/wqflask/tests/unit/wqflask/wgcna/__init__.py
new file mode 100644
index 00000000..e69de29b
--- /dev/null
+++ b/wqflask/tests/unit/wqflask/wgcna/__init__.py
diff --git a/wqflask/tests/unit/wqflask/wgcna/test_wgcna.py b/wqflask/tests/unit/wqflask/wgcna/test_wgcna.py
new file mode 100644
index 00000000..8e947e2f
--- /dev/null
+++ b/wqflask/tests/unit/wqflask/wgcna/test_wgcna.py
@@ -0,0 +1,50 @@
+
+"""module contains for processing gn3 wgcna data"""
+from unittest import TestCase
+
+from wqflask.wgcna.gn3_wgcna import process_wgcna_data
+
+
+class DataProcessingTests(TestCase):
+ """class contains data processing tests"""
+
+ def test_data_processing(self):
+ """test for parsing data for datatable"""
+ output = {
+ "input": {
+ "sample_names": ["BXD1", "BXD2", "BXD3", "BXD4", "BXD5", "BXD6"],
+
+ },
+ "output": {
+ "ModEigens": {
+ "MEturquoise": [
+ 0.0646677768085351,
+ 0.137200224277058,
+ 0.63451113720732,
+ -0.544002665501479,
+ -0.489487590361863,
+ 0.197111117570427
+ ],
+ "MEgrey": [
+ 0.213,
+ 0.214,
+ 0.3141,
+ -0.545,
+ -0.423,
+ 0.156,
+ ]
+ }}}
+
+ row_data = [['BXD1', 0.065, 0.213],
+ ['BXD2', 0.137, 0.214],
+ ['BXD3', 0.635, 0.314],
+ ['BXD4', -0.544, -0.545],
+ ['BXD5', -0.489, -0.423],
+ ['BXD6', 0.197, 0.156]]
+
+ expected_results = {
+ "col_names": ["sample_names", "MEturquoise", "MEgrey"],
+ "mod_dataset": row_data
+ }
+
+ self.assertEqual(process_wgcna_data(output), expected_results)