Merge branch 'testing' of github.com:genenetwork/genenetwork2 into feature/add_rqtl_pairscan

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)