G3-9 Initial

pyproject.toml

@@ -8,10 +8,17 @@ packages = [
 ]
 
 [tool.poetry.dependencies]
-python = "^3.9"
+#python = "^3.9"
+python = "^3.10.9"
+
 geneweaver-core = "^0.8.0a0"
 fastapi = {extras = ["all"], version = "^0.99.1"}
-uvicorn = {extras = ["standard"], version = "^0.24.0"}
+uvicorn = {extras = ["standard"], version = "^0.23.2"}
+
+#fastapi = "^0.79.0"
+#fastapi = {version = "^0.79.0"}
+#uvicorn = {extras = ["standard"], version = "^0.18.2"}
+
 geneweaver-db = "^0.2.0a0"
 psycopg-pool = "^3.1.7"
 requests = "^2.31.0"
@@ -20,6 +27,7 @@ python-jose = {extras = ["cryptography"], version = "^3.3.0"}
 [tool.poetry.group.dev.dependencies]
 geneweaver-testing = "^0.0.3"
 pytest-asyncio = "^0.21.0"
+magicmock =  "^0.03"
 
 [tool.ruff]
 select = ['F', 'E', 'W', 'A', 'C90', 'N', 'B', 'ANN', 'D', 'I', 'ERA', 'PD', 'NPY', 'PT']

src/geneweaver/api/controller/genesets.py

@@ -2,15 +2,17 @@
 from typing import Optional
 
 from fastapi import APIRouter, Depends, HTTPException, Security
-from geneweaver.api import dependencies as deps
-from geneweaver.api.schemas.auth import UserInternal
+from fastapi.logger import logger
 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
 
-router = APIRouter(prefix="/genesets")
+from geneweaver.api import dependencies as deps
+from geneweaver.api.schemas.auth import UserInternal
+from geneweaver.api.services import geneset as genset_service
+from . import message as api_message
 
+router = APIRouter(prefix="/genesets")
 
 @router.get("")
 def get_visible_genesets(
@@ -26,16 +28,23 @@ def get_visible_genesets(
 def get_geneset(
     geneset_id: int,
     user: UserInternal = Security(deps.full_user),
-    cursor: Optional[deps.Cursor] = Depends(deps.cursor),
+    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")
+    try:
+        response = genset_service.get_geneset(geneset_id, user, cursor)
+
+    except Exception as err:
+        logger.error(err)
+        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}
+    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.ACCESS_FORBIDEN)
 
+    return response
 
 @router.post("")
 def upload_geneset(

src/geneweaver/api/controller/message.py

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

src/geneweaver/api/core/config_class.py

@@ -38,7 +38,7 @@ def assemble_db_connection(
         "openid profile email": "read",
     }
     JWT_PERMISSION_PREFIX: str = "approle"
-    AUTH_CLIENT_ID: str = "oVm9omUtLBpVyL7YfJA8gp3hHaHwyVt8"
+    AUTH_CLIENT_ID: str = "T7bj6wlmtVcAN2O6kzDRwPVFyIj4UQNs"
 
     class Config:
         """Configuration for the BaseSettings class."""

src/geneweaver/api/services/geneset.py

@@ -1 +1,46 @@
 """Service functions for dealing with genesets."""
+
+from fastapi.logger import logger
+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 geneweaver.api import dependencies as deps
+from geneweaver.api.controller import message
+from geneweaver.api.schemas.auth import User
+
+
+def get_geneset(
+    geneset_id: int,
+    user: User,
+    cursor: deps.Cursor
+) -> dict:
+
+    """Get a geneset by ID."""
+    try:
+        if not is_geneset_readable_by_user(geneset_id, user, cursor):
+            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(
+        geneset_id: int,
+        user: User,
+        cursor: deps.Cursor
+) -> 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/.pytest_cache/.gitignore

@@ -0,0 +1,2 @@
+# Created by pytest automatically.
+v

tests/controllers/.pytest_cache/CACHEDIR.TAG

@@ -0,0 +1,4 @@
+Signature: 8a477f597d28d172789f06886806bc55
+# This file is a cache directory tag created by pytest.
+# For information about cache directory tags, see:
+#	https://bford.info/cachedir/spec.html

tests/controllers/.pytest_cache/README.md

@@ -0,0 +1,8 @@
+# pytest cache directory #
+
+This directory contains data from the pytest's cache plugin,
+which provides the `--lf` and `--ff` options, as well as the `cache` fixture.
+
+**Do not** commit this to version control.
+
+See [the docs](https://docs.pytest.org/en/stable/how-to/cache.html) for more information.

tests/controllers/test_genesets.py

@@ -0,0 +1,72 @@
+import importlib.resources
+import json
+from unittest.mock import Mock
+from unittest.mock import patch
+
+import psycopg
+import pytest
+from fastapi.testclient import TestClient
+
+from geneweaver.api.dependencies import full_user, cursor
+from geneweaver.api.main import app
+
+client = TestClient(app)
+
+### 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
+m1 = Mock()
+def mock_full_user() -> m1.AsyncMock:
+    return m1
+m2 = Mock()
+def mock_cursor() -> psycopg.Cursor:
+    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")
+    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):
+    mock_genset_is_readable.return_value = True
+    mock_get_genenset.return_value = test_data
+
+    response = client.get("/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):
+
+    mock_genset_is_readable.return_value = False
+    response = client.get("/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):
+
+    mock_genset_is_readable.side_effect = Exception
+
+    with pytest.raises(Exception):
+        response = client.get("/genesets/1234")
+        assert response.json() == {'detail': 'Unexpected error'}
+        assert response.status_code == 500

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 +1,68 @@
+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
+
+## 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_no_errors(mock_genset_readable_func, mock_db_geneset, mock_db_genset_value):
+
+    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
+
+
+@patch('geneweaver.api.services.geneset.is_geneset_readable_by_user')
+def test_get_geneset_no_user_access(mock_genset_readable_func):
+
+    mock_genset_readable_func.return_value = False
+    response = geneset.get_geneset(1234, None, None)
+    assert response.get('error') == 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):
+
+    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(1234, None, 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):
+
+    mock_genset_is_readable.return_value = True
+    response = geneset.is_geneset_readable_by_user(1234, mock_user, None)
+    assert response == 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):
+    mock_genset_is_readable.sideEffect = Exception
+
+    with pytest.raises(Exception):
+        geneset.is_geneset_readable_by_user(1234, mock_user, None)
+
+