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--git a/src/geneweaver/api/controller/api.py b/src/geneweaver/api/controller/api.py index 062a366..e004e0d 100644 --- a/src/geneweaver/api/controller/api.py +++ b/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) diff --git a/src/geneweaver/api/controller/message.py b/src/geneweaver/api/controller/message.py index 88f6256..6aab170 100644 --- a/src/geneweaver/api/controller/message.py +++ b/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" diff --git a/src/geneweaver/api/controller/monitors.py b/src/geneweaver/api/controller/monitors.py new file mode 100644 index 0000000..b0cc37d --- /dev/null +++ b/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 diff --git a/src/geneweaver/api/services/monitors.py b/src/geneweaver/api/services/monitors.py new file mode 100644 index 0000000..2b83a3d --- /dev/null +++ b/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 diff --git a/tests/controllers/test_monitor.py b/tests/controllers/test_monitor.py new file mode 100644 index 0000000..c4bbec5 --- /dev/null +++ b/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 diff --git a/tests/data/__init__.py b/tests/data/__init__.py index 8c07089..13f3dd2 100644 --- a/tests/data/__init__.py +++ b/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 diff --git a/tests/data/monitors.json b/tests/data/monitors.json new file mode 100644 index 0000000..a8c85d8 --- /dev/null +++ b/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 + } + } + } +} \ No newline at end of file diff --git a/tests/services/test_monitors.py b/tests/services/test_monitors.py new file mode 100644 index 0000000..5bc035f --- /dev/null +++ b/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)