G3-9 unit tests, linting

pyproject.toml

@@ -8,17 +8,11 @@ packages = [
 ]
 
 [tool.poetry.dependencies]
-#python = "^3.9"
-python = "^3.10.9"
+python = "^3.9"
 
 geneweaver-core = "^0.8.0a0"
 fastapi = {extras = ["all"], version = "^0.99.1"}
-uvicorn = {extras = ["standard"], version = "^0.23.2"}
-
-#fastapi = "^0.79.0"
-#fastapi = {version = "^0.79.0"}
-#uvicorn = {extras = ["standard"], version = "^0.18.2"}
-
+uvicorn = {extras = ["standard"], version = "^0.24.0"}
 geneweaver-db = "^0.2.0a0"
 psycopg-pool = "^3.1.7"
 requests = "^2.31.0"
@@ -28,6 +22,7 @@ python-jose = {extras = ["cryptography"], version = "^3.3.0"}
 geneweaver-testing = "^0.0.3"
 pytest-asyncio = "^0.21.0"
 magicmock =  "^0.03"
+pylint= "^3.0.3"
 
 [tool.ruff]
 select = ['F', 'E', 'W', 'A', 'C90', 'N', 'B', 'ANN', 'D', 'I', 'ERA', 'PD', 'NPY', 'PT']

src/geneweaver/api/controller/genesets.py

@@ -42,7 +42,7 @@ def get_geneset(
         if response.get("message") == api_message.ACCESS_FORBIDEN:
             raise HTTPException(status_code=403, detail=api_message.ACCESS_FORBIDEN)
         else:
-            raise HTTPException(status_code=500, detail=api_message.ACCESS_FORBIDEN)
+            raise HTTPException(status_code=500, detail=api_message.UNEXPECTED_ERROR)
 
     return response
 

src/geneweaver/api/controller/message.py

@@ -1,6 +1,6 @@
-"""Costant key/value messages"""
+"""Constants key/value messages"""
 
 
 ##Errors
 ACCESS_FORBIDEN="Forbidden"
-UNEXPECTED_ERROR="Unexpected Error"
+UNEXPECTED_ERROR="Unexpected Error"

src/geneweaver/api/services/geneset.py

@@ -43,4 +43,4 @@ def is_geneset_readable_by_user(
         logger.error(err)
         raise err
 
-    return readable
+    return readable

tests/controllers/test_genesets.py

@@ -1,3 +1,5 @@
+""" Tests for geneset API"""
+
 import importlib.resources
 import json
 from unittest.mock import Mock
@@ -23,50 +25,54 @@
 response_mock.json.return_value = test_data
 
 ### Mock dependencies
-m1 = Mock()
-def mock_full_user() -> m1.AsyncMock:
-    return m1
-m2 = Mock()
+def mock_full_user() -> Mock:
+    """ User auth mock"""
+    m1 = Mock()
+    return m1.AsyncMock()
+
 def mock_cursor() -> psycopg.Cursor:
+    """ DB cursor mock"""
+    m2 = Mock()
     return m2.AsyncMock()
-m3 = Mock()
-def mock_cursor_obj() -> psycopg.Cursor:
-    return m3.AsyncMock()
 
 app.dependency_overrides.update(
     {full_user: mock_full_user, cursor: mock_cursor}
 )
 
 @patch.object(client, 'get', return_value=response_mock)
 def test_get_geneset(mock_client):
-    response = client.get("/genesets/1234")
+    """ test get request for geneset ID"""
+    response = client.get("/api/genesets/1234")
     assert response.status_code == 200
 
 @patch('geneweaver.api.services.geneset.get_geneset')
 @patch('geneweaver.api.services.geneset.is_geneset_readable_by_user')
 def test_get_geneset_response(mock_genset_is_readable, mock_get_genenset):
+    """ test get geneset ID data response"""
     mock_genset_is_readable.return_value = True
     mock_get_genenset.return_value = test_data
 
-    response = client.get("/genesets/1234")
+    response = client.get("/api/genesets/1234")
     assert response.status_code == 200
     assert response.json() == test_data
 
 @patch('geneweaver.api.services.geneset.db_is_readable')
 def test_get_geneset_forbidden(mock_genset_is_readable):
+    """ test forbidden response"""
 
     mock_genset_is_readable.return_value = False
-    response = client.get("/genesets/1234")
+    response = client.get("/api/genesets/1234")
 
     assert response.json() == {'detail': 'Forbidden'}
     assert response.status_code == 403
 
 @patch('geneweaver.api.services.geneset.db_is_readable')
 def test_get_geneset_unexpected_error(mock_genset_is_readable):
+    """ test unexpected error response"""
 
     mock_genset_is_readable.side_effect = Exception
 
     with pytest.raises(Exception):
-        response = client.get("/genesets/1234")
+        response = client.get("/api/genesets/1234")
         assert response.json() == {'detail': 'Unexpected error'}
         assert response.status_code == 500

tests/services/test_genset.py

@@ -1,11 +1,13 @@
+""" Tests for geneset Service"""
+
 import importlib.resources
 import json
 from unittest.mock import patch
 
 import pytest
 
-import geneweaver.api.controller.message as message
-import geneweaver.api.services.geneset as geneset
+from geneweaver.api.controller import message
+from geneweaver.api.services import geneset
 
 ## Load test data
 # Opening JSON file
@@ -16,28 +18,33 @@
 @patch('geneweaver.api.services.geneset.db_geneset')
 @patch('geneweaver.api.services.geneset.db_geneset_value')
 @patch('geneweaver.api.services.geneset.is_geneset_readable_by_user')
-def test_get_geneset_no_errors(mock_genset_readable_func, mock_db_geneset, mock_db_genset_value):
+def test_get_geneset(mock_genset_readable_func, mock_db_geneset, mock_db_genset_value):
+    """ test basic get geneset by ID"""
 
     mock_genset_readable_func.return_value = True
     mock_db_geneset.by_id.return_value = {}
     mock_db_genset_value.by_id.return_value = {}
     response = geneset.get_geneset(1234, None, None)
-    assert response.get('error') == None
+    assert response.get('error') is None
 
 
 @patch('geneweaver.api.services.geneset.is_geneset_readable_by_user')
 def test_get_geneset_no_user_access(mock_genset_readable_func):
+    """ test get geneset by ID with no user access"""
 
     mock_genset_readable_func.return_value = False
     response = geneset.get_geneset(1234, None, None)
-    assert response.get('error') == True
+    assert response.get('error') is True
     assert response.get('message') == message.ACCESS_FORBIDEN
 
 
 @patch('geneweaver.api.services.geneset.db_geneset')
 @patch('geneweaver.api.services.geneset.db_geneset_value')
 @patch('geneweaver.api.services.geneset.is_geneset_readable_by_user')
-def test_get_geneset_returned_values(mock_genset_readable_func, mock_db_genset_value, mock_db_geneset):
+def test_get_geneset_returned_values(mock_genset_readable_func,
+                                     mock_db_genset_value,
+                                     mock_db_geneset):
+    """ test get geneset by ID data response structure"""
 
     mock_genset_readable_func.return_value = True
     mock_db_geneset.by_id.return_value = test_data.get('geneset')
@@ -51,18 +58,19 @@ def test_get_geneset_returned_values(mock_genset_readable_func, mock_db_genset_v
 @patch('geneweaver.api.services.geneset.db_is_readable')
 @patch('geneweaver.api.services.geneset.User')
 def test_is_redable_by_user(mock_user, mock_genset_is_readable):
+    """ test is geneset ID readable by passed user"""
 
     mock_genset_is_readable.return_value = True
     response = geneset.is_geneset_readable_by_user(1234, mock_user, None)
-    assert response == True
+    assert response is True
 
 
 @patch('geneweaver.db.geneset.is_readable')
 @patch('geneweaver.api.services.geneset.User')
 def test_is_redable_by_user_error(mock_user, mock_genset_is_readable):
+    """ test is geneset ID readable with server error"""
+
     mock_genset_is_readable.sideEffect = Exception
 
     with pytest.raises(Exception):
         geneset.is_geneset_readable_by_user(1234, mock_user, None)
-
-