Merge pull request #74 from TheJacksonLaboratory/G3-271-health-check-…

…enpoint

G3-271 server health check endpoint

.github/workflows/_format-lint-action.yml

@@ -19,6 +19,6 @@ jobs:
       - name: Install Black and Ruff
         run: pip install black ruff
       - name: Run Ruff Linter
-        run: ruff src/ tests/
+        run: ruff check src/ tests/
       - name: Run Black Formatter
         run: black src/ tests/

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "geneweaver-api"
-version = "0.7.0a2"
+version = "0.7.0a3"
 description = "The Geneweaver API"
 authors = [
     "Alexander Berger <[email protected]>",
@@ -20,7 +20,7 @@ python = "^3.9"
 geneweaver-core = "^0.10.0a2"
 fastapi = {extras = ["all"], version = "^0.99.1"}
 uvicorn = {extras = ["standard"], version = "^0.24.0"}
-geneweaver-db = "0.5.0a2"
+geneweaver-db = "0.5.0a8"
 psycopg-pool = "^3.1.7"
 requests = "^2.31.0"
 python-jose = {extras = ["cryptography"], version = "^3.3.0"}

src/geneweaver/api/controller/api.py

@@ -7,7 +7,14 @@
 from fastapi import APIRouter, FastAPI, Security
 from geneweaver.api import __version__
 from geneweaver.api import dependencies as deps
-from geneweaver.api.controller import genes, genesets, publications, search, species
+from geneweaver.api.controller import (
+    genes,
+    genesets,
+    monitors,
+    publications,
+    search,
+    species,
+)
 from geneweaver.api.core.config import settings
 
 app = FastAPI(
@@ -31,5 +38,6 @@
 api_router.include_router(publications.router)
 api_router.include_router(species.router)
 api_router.include_router(search.router)
+api_router.include_router(monitors.router)
 
 app.include_router(api_router, prefix=settings.API_PREFIX)

src/geneweaver/api/controller/message.py

@@ -26,3 +26,4 @@
 GS_PUB_SEARCH_TEXT = (
     "Gensets and/or publications search types ('genesets', 'publications') "
 )
+CHECK_DB_HEALTH = "Check DB health flag"

src/geneweaver/api/controller/monitors.py

@@ -0,0 +1,29 @@
+"""Endpoints related to system health."""
+
+from typing import Optional
+
+from fastapi import APIRouter, Depends, Query
+from geneweaver.api import dependencies as deps
+from geneweaver.api.services import monitors as monitors_service
+from typing_extensions import Annotated
+
+from . import message as api_message
+
+router = APIRouter(prefix="/monitors", tags=["monitors"])
+
+
+@router.get("/servers/health")
+def get_health_check(
+    cursor: Optional[deps.Cursor] = Depends(deps.cursor),
+    db_health_check: Annotated[
+        Optional[bool], Query(description=api_message.CHECK_DB_HEALTH)
+    ] = False,
+) -> dict:
+    """Return 200 API response if reachable and optionally check db health."""
+    response = {"status": "UP"}
+
+    if db_health_check:
+        db_health_response = monitors_service.check_db_health(cursor)
+        response["DB_status"] = db_health_response
+
+    return response

src/geneweaver/api/services/monitors.py

@@ -0,0 +1,20 @@
+"""Service monitors for system health."""
+
+from fastapi.logger import logger
+from geneweaver.db.monitor.db_health import health_check as db_health_check
+from psycopg import Cursor
+
+
+def check_db_health(cursor: Cursor) -> dict:
+    """Check DB health status.
+
+    @param cursor: DB cursor
+    @return: db health response (dict).
+    """
+    try:
+        results = db_health_check(cursor)
+        return results
+
+    except Exception as err:
+        logger.error(err)
+        raise err

tests/controllers/test_monitor.py

@@ -0,0 +1,23 @@
+"""Tests for system monitor apis."""
+
+from unittest.mock import patch
+
+from tests.data import test_monitors_data
+
+db_health_status = test_monitors_data.get("db_health_status")
+
+
+@patch("geneweaver.api.services.monitors.check_db_health")
+def test_valid_url_req(mock_db_heath_service_call, client):
+    """Test valid url request to get system health status."""
+    response = client.get(
+        url="/api/monitors/servers/health", params={"db_health_check": False}
+    )
+    assert response.status_code == 200
+
+    mock_db_heath_service_call.return_value = db_health_status.get("DB_status")
+    response = client.get(
+        url="/api/monitors/servers/health", params={"db_health_check": True}
+    )
+    assert response.status_code == 200
+    assert response.json() == db_health_status

tests/data/__init__.py

@@ -32,6 +32,8 @@
 
 genes_json = importlib.resources.read_text("tests.data", "genes.json")
 
+monitors_json = importlib.resources.read_text("tests.data", "monitors.json")
+
 ## laod and returns JSON string as a dictionary
 
 # geneset test data
@@ -134,6 +136,12 @@
 }
 
 
+## monitors test data
+test_monitors_data = {
+    "db_health_status": json.loads(monitors_json).get("db_health_status"),
+}
+
+
 def get_species_db_resp(species_data: list) -> list:
     """Get species data as returned by DB."""
     species = species_data

tests/data/monitors.json

@@ -0,0 +1,16 @@
+{
+  "db_health_status": {
+    "status": "UP",
+    "DB_status": {
+      "gene_identifier_last_update": {
+        "gi_date": "2024-06-24T01:54:48.023015+00:00"
+      },
+      "gene_count": {
+        "count": 16
+      },
+      "geneset_count": {
+        "count": 272143
+      }
+    }
+  }
+}

tests/services/test_monitors.py

@@ -0,0 +1,28 @@
+"""Tests for system monitor services."""
+
+from unittest.mock import patch
+
+import pytest
+from geneweaver.api.services import monitors
+
+from tests.data import test_monitors_data
+
+db_health_status = test_monitors_data.get("db_health_status")
+
+
+@patch("geneweaver.api.services.monitors.db_health_check")
+def test_db_health_check(mock_db_heath):
+    """Test call to get db health status."""
+    mock_db_heath.return_value = db_health_status.get("DB_status")
+    response = monitors.check_db_health(None)
+
+    assert response == db_health_status.get("DB_status")
+
+
+@patch("geneweaver.api.services.monitors.db_health_check")
+def test_db_health_check_error(mock_db_heath):
+    """Test error in call to get db health status."""
+    mock_db_heath.side_effect = Exception("ERROR")
+
+    with pytest.raises(expected_exception=Exception):
+        monitors.check_db_health(None)