More tests

README.md

@@ -1,3 +1,5 @@
+[![codecov](https://codecov.io/gh/BioPack-team/shepherd/graph/badge.svg?token=NTPV9WF7EO)](https://codecov.io/gh/BioPack-team/shepherd)
+
 # Translator Shepherd Service
 
 Shepherd is a shared platform for ARA implementation. Incorporated ARAs have access to a plethora of shared ARA functionality while retaining the ability to implement their own custom operations.

test-requirements.txt

@@ -1,4 +1,5 @@
 fakeredis
+httpx
 pytest
 pytest-asyncio
 pytest-cov

tests/conftest.py

@@ -0,0 +1,42 @@
+"""Import pytest fixtures."""
+
+import fakeredis.aioredis as fakeredis
+from psycopg_pool import AsyncConnectionPool
+import pytest
+import pytest_asyncio
+import redis.asyncio as aioredis
+from unittest.mock import AsyncMock, MagicMock
+
+
+@pytest.fixture
+def postgres_mock():
+    """
+    Factory for creating a mock postgres pool with custom return value.
+    """
+
+    def _create_mock(return_value):
+        mock_conn = AsyncMock()
+        mock_conn.execute.side_effect = return_value
+
+        mock_pool = AsyncMock(spec=AsyncConnectionPool)
+        mock_pool.connection.return_value.__aenter__.return_value = mock_conn
+        mock_pool.connection.return_value.__aexit__.return_value = None
+
+        return mock_conn, mock_pool
+
+    return _create_mock
+
+
+@pytest.fixture()
+def redis_mock(monkeypatch):
+    """
+    Create a fake redis client and function for getting that client.
+    """
+    fake_redis = fakeredis.FakeRedis(decode_responses=True)
+
+    def mock_redis_constructor(*args, **kwargs):
+        return fake_redis
+
+    monkeypatch.setattr(aioredis, "Redis", mock_redis_constructor)
+
+    return fake_redis

tests/unit/test_example.py

@@ -3,14 +3,15 @@
 import pytest
 import redis.asyncio
 from shepherd_utils.broker import get_task
+
 from workers.example_ara.worker import example_ara
-from tests.helpers.mock_redis import redis_mock
+from workers.example_lookup.worker import example_lookup
 
 
 @pytest.mark.asyncio
-async def test_example(monkeypatch, mocker):
-    _, redis_constructor = await redis_mock()
-    monkeypatch.setattr(redis.asyncio, "Redis", redis_constructor)
+async def test_example(redis_mock):
+    # _, redis_constructor = await redis_mock()
+    # monkeypatch.setattr(redis.asyncio, "Redis", redis_constructor)
     logger = logging.getLogger(__name__)
 
     await example_ara(["test", {"query_id": "test"}], logger)
@@ -28,3 +29,43 @@ async def test_example(monkeypatch, mocker):
         "filter_results_top_n",
         "filter_kgraph_orphans",
     ] == [op["id"] for op in workflow]
+
+
+@pytest.mark.asyncio
+async def test_example_lookup(mocker, redis_mock):
+    mock_callback_id = mocker.patch("workers.example_lookup.worker.add_callback_id")
+    mock_callback_id.return_value = "test"
+    mock_callback_response = mocker.patch(
+        "workers.example_lookup.worker.save_callback_response"
+    )
+    mock_callback_response.return_value = {}
+    mock_running_callbacks = mocker.patch(
+        "workers.example_lookup.worker.get_running_callbacks"
+    )
+    mock_running_callbacks.return_value = []
+    mock_response = mocker.Mock()
+    mocker.patch("httpx.AsyncClient.post", return_value=mock_response)
+    logger = logging.getLogger(__name__)
+
+    await example_lookup(
+        [
+            "test",
+            {
+                "query_id": "test",
+                "workflow": json.dumps(
+                    [{"id": "example.lookup"}, {"id": "example.score"}]
+                ),
+            },
+        ],
+        logger,
+    )
+
+    # Get the task that the ara should have put on the queue
+    task = await get_task("example.score", "consumer", "test", logger)
+    assert task is not None
+    workflow = json.loads(task[1]["workflow"])
+    # make sure the workflow was correctly passed
+    assert len(workflow) == 1
+    assert [
+        "example.score",
+    ] == [op["id"] for op in workflow]

workers/example_lookup/worker.py

@@ -4,6 +4,7 @@
 import httpx
 import json
 import logging
+from pathlib import Path
 import time
 import uuid
 from shepherd_utils.db import (
@@ -30,7 +31,8 @@ async def example_lookup(task, logger: logging.Logger):
     # Do query expansion or whatever lookup process
     # We're going to stub a response
     start = time.time()
-    with open("test_response.json", "r") as f:
+    test_response = Path(__file__).parent / "test_response.json"
+    with open(test_response, "r") as f:
         response = json.load(f)
     logger.debug(f"Loading json took {time.time() - start}")