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b/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'] diff --git a/src/geneweaver/api/controller/genesets.py b/src/geneweaver/api/controller/genesets.py index ad09b50..fbd63e8 100644 --- a/src/geneweaver/api/controller/genesets.py +++ b/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 diff --git a/src/geneweaver/api/controller/message.py b/src/geneweaver/api/controller/message.py index add6cf4..4304184 100644 --- a/src/geneweaver/api/controller/message.py +++ b/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" \ No newline at end of file +UNEXPECTED_ERROR="Unexpected Error" diff --git a/src/geneweaver/api/services/geneset.py b/src/geneweaver/api/services/geneset.py index 67cd66c..e1d8013 100644 --- a/src/geneweaver/api/services/geneset.py +++ b/src/geneweaver/api/services/geneset.py @@ -43,4 +43,4 @@ def is_geneset_readable_by_user( logger.error(err) raise err - return readable \ No newline at end of file + return readable diff --git a/tests/controllers/test_genesets.py b/tests/controllers/test_genesets.py index 1b25fb0..7451765 100644 --- a/tests/controllers/test_genesets.py +++ b/tests/controllers/test_genesets.py @@ -1,3 +1,5 @@ +""" Tests for geneset API""" + import importlib.resources import json from unittest.mock import Mock @@ -23,15 +25,15 @@ 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} @@ -39,34 +41,38 @@ def mock_cursor_obj() -> psycopg.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 diff --git a/tests/services/test_genset.py b/tests/services/test_genset.py index 276db56..a37f824 100644 --- a/tests/services/test_genset.py +++ b/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) - -