Merge pull request #7 from TheJacksonLaboratory/G3-9-get-geneset-by-i…

…d-endpoint

G3 9 get geneset by id endpoint

README.MD

@@ -25,6 +25,28 @@ virtualenv activated, or just run `poetry run uvicorn geneweaver.api.main:app --
 This will host the application on `http://127.0.0.1:8000/` which means the swagger docs
 page is available at `http://127.0.0.1:8000/docs`.
 
+### Code linters
+
+Ruff rules: (https://docs.astral.sh/ruff/rules/)
+
+From active local environment on command line run:
+
+    ruff src/ tests/ --fix
+
+then run black (code formatter: https://black.readthedocs.io/en/stable/the_black_code_style/current_style.html)
+
+    black src/ tests/
+
+### Unit test
+
+Create appropriate test per code modifications without dependencies to external resources 
+such as DB, Webserver, or APIs. Create appropriate mocks for external resources and data as needed.
+
+    Tests directory: geneweaver-api/tests
+
+To execute tests, from the command line run:
+
+    pytest 
 
 ### Continuous Integration & Deployment
 When a PR is crated in GitHub, it will automatically trigger a workflow that will run 

pyproject.toml

@@ -9,6 +9,7 @@ packages = [
 
 [tool.poetry.dependencies]
 python = "^3.9"
+
 geneweaver-core = "^0.8.0a0"
 fastapi = {extras = ["all"], version = "^0.99.1"}
 uvicorn = {extras = ["standard"], version = "^0.24.0"}

src/geneweaver/api/controller/genesets.py

@@ -4,10 +4,12 @@
 from fastapi import APIRouter, Depends, HTTPException, Security
 from geneweaver.api import dependencies as deps
 from geneweaver.api.schemas.auth import UserInternal
+from geneweaver.api.services import geneset as genset_service
 from geneweaver.core.schema.geneset import GenesetUpload
 from geneweaver.db import geneset as db_geneset
 from geneweaver.db import geneset_value as db_geneset_value
-from geneweaver.db.geneset import is_readable
+
+from . import message as api_message
 
 router = APIRouter(prefix="/genesets")
 
@@ -29,12 +31,15 @@ def get_geneset(
     cursor: Optional[deps.Cursor] = Depends(deps.cursor),
 ) -> dict:
     """Get a geneset by ID."""
-    if not is_readable(cursor, user.id, geneset_id):
-        raise HTTPException(status_code=403, detail="Forbidden")
+    response = genset_service.get_geneset(cursor, geneset_id, user)
+
+    if "error" in response:
+        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.UNEXPECTED_ERROR)
 
-    geneset = db_geneset.by_id(cursor, geneset_id)
-    geneset_values = db_geneset_value.by_geneset_id(cursor, geneset_id)
-    return {"geneset": geneset, "geneset_values": geneset_values}
+    return response
 
 
 @router.post("")

src/geneweaver/api/controller/message.py

@@ -0,0 +1,6 @@
+"""Constants key/value messages."""
+
+
+##Errors
+ACCESS_FORBIDEN = "Forbidden"
+UNEXPECTED_ERROR = "Unexpected Error"

src/geneweaver/api/services/geneset.py

@@ -1 +1,36 @@
 """Service functions for dealing with genesets."""
+
+from fastapi.logger import logger
+from geneweaver.api.controller import message
+from geneweaver.api.schemas.auth import User
+from geneweaver.db import geneset as db_geneset
+from geneweaver.db import geneset_value as db_geneset_value
+from geneweaver.db.geneset import is_readable as db_is_readable
+from psycopg import Cursor
+
+
+def get_geneset(cursor: Cursor, geneset_id: int, user: User) -> dict:
+    """Get a geneset by ID."""
+    try:
+        if not is_geneset_readable_by_user(cursor, geneset_id, user):
+            return {"error": True, "message": message.ACCESS_FORBIDEN}
+
+        geneset = db_geneset.by_id(cursor, geneset_id)
+        geneset_values = db_geneset_value.by_geneset_id(cursor, geneset_id)
+        return {"geneset": geneset, "geneset_values": geneset_values}
+
+    except Exception as err:
+        logger.error(err)
+        raise err
+
+
+def is_geneset_readable_by_user(cursor: Cursor, geneset_id: int, user: User) -> bool:
+    """Check if the user can read the geneset from DB."""
+    readable: bool = False
+    try:
+        readable = db_is_readable(cursor, user.id, geneset_id)
+    except Exception as err:
+        logger.error(err)
+        raise err
+
+    return readable

tests/controllers/__init__.py

@@ -0,0 +1 @@
+"""Tests for controllers."""

tests/controllers/conftest.py

@@ -0,0 +1,68 @@
+"""Fixtures for the controller tests."""
+import importlib.resources
+import json
+from unittest.mock import Mock
+
+import psycopg
+import pytest
+from fastapi.testclient import TestClient
+from geneweaver.api.core.config_class import GeneweaverAPIConfig
+
+# Load test data
+# Opening JSON file
+str_json = importlib.resources.read_text("tests.data", "response_geneset_1234.json")
+# returns JSON string as a dictionary
+test_data = json.loads(str_json)
+
+response_mock = Mock()
+response_mock.status_code = 200
+response_mock.json.return_value = test_data
+
+
+# Mock dependencies
+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()
+
+
+@pytest.fixture()
+def mock_settings(monkeypatch) -> GeneweaverAPIConfig:
+    """Patch the settings class to return a test settings instance.
+
+    returns: A patched settings instance.
+    """
+    test_settings = GeneweaverAPIConfig(
+        DB_HOST="localhost",
+        DB_USERNAME="postgres",
+        DB_PASSWORD="postgres",
+        DB_NAME="geneweaver",
+    )
+
+    monkeypatch.setattr(
+        "geneweaver.api.core.config_class.GeneweaverAPIConfig", lambda: test_settings
+    )
+
+    return test_settings
+
+
+@pytest.fixture()
+def client(mock_settings) -> TestClient:
+    """Provide a mocked FastAPI application.
+
+    returns: A mocked FastAPI application.
+    """
+    from geneweaver.api.dependencies import cursor, full_user
+    from geneweaver.api.main import app
+
+    test_app = TestClient(app)
+
+    app.dependency_overrides.update({full_user: mock_full_user, cursor: mock_cursor})
+
+    return test_app

tests/controllers/test_genesets.py

@@ -0,0 +1,37 @@
+"""Tests for geneset API."""
+from unittest.mock import patch
+
+import pytest
+
+from tests.controllers.conftest import test_data
+
+
+@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, client):
+    """Test get geneset ID data response."""
+    mock_genset_is_readable.return_value = True
+    mock_get_genenset.return_value = test_data
+
+    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, client):
+    """Test forbidden response."""
+    mock_genset_is_readable.return_value = False
+    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, client):
+    """Test unexpected error response."""
+    mock_genset_is_readable.side_effect = Exception
+
+    with pytest.raises(expected_exception=Exception):
+        client.get("/api/genesets/1234")

tests/data/__init__.py

@@ -0,0 +1 @@
+"""Data package for tests."""

tests/data/response_geneset_1234.json

@@ -0,0 +1,50 @@
+{
+  "geneset": null,
+  "geneset_values": [
+    {
+      "gs_id": 1234,
+      "ode_gene_id": 70495,
+      "gsv_value": 1,
+      "gsv_hits": 1,
+      "gsv_source_list": [
+        "PDE4DIP"
+      ],
+      "gsv_value_list": [
+        1
+      ],
+      "gsv_in_threshold": true,
+      "gsv_date": "2020-05-05",
+      "ode_ref_id": "PDE4DIP"
+    },
+    {
+      "gs_id": 1234,
+      "ode_gene_id": 83819,
+      "gsv_value": 1,
+      "gsv_hits": 1,
+      "gsv_source_list": [
+        "TMEPAI"
+      ],
+      "gsv_value_list": [
+        1
+      ],
+      "gsv_in_threshold": true,
+      "gsv_date": "2020-05-05",
+      "ode_ref_id": "PMEPA1"
+    },
+    {
+      "gs_id": 1234,
+      "ode_gene_id": 90284,
+      "gsv_value": 1,
+      "gsv_hits": 1,
+      "gsv_source_list": [
+        "PREPL"
+      ],
+      "gsv_value_list": [
+        1
+      ],
+      "gsv_in_threshold": true,
+      "gsv_date": "2020-05-05",
+      "ode_ref_id": "PREPL"
+    }
+  ]
+}

tests/services/test_genset.py

@@ -0,0 +1,71 @@
+"""Tests for geneset Service."""
+
+import importlib.resources
+import json
+from unittest.mock import patch
+
+import pytest
+from geneweaver.api.controller import message
+from geneweaver.api.services import geneset
+
+## Load test data
+# Opening JSON file
+str_json = importlib.resources.read_text("tests.data", "response_geneset_1234.json")
+# returns JSON string as a dictionary
+test_data = json.loads(str_json)
+
+
+@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(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(None, 1234, 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(None, 1234, None)
+    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
+):
+    """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")
+    mock_db_genset_value.by_geneset_id.return_value = test_data.get("geneset_values")
+    response = geneset.get_geneset(None, 1234, None)
+
+    assert response.get("genset") == test_data["geneset"]
+    assert response.get("geneset_values") == test_data["geneset_values"]
+
+
+@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(None, 1234, mock_user)
+    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(expected_exception=Exception):
+        geneset.is_geneset_readable_by_user(None, 1234, mock_user)