aboutsummaryrefslogtreecommitdiff
path: root/tests
diff options
context:
space:
mode:
Diffstat (limited to 'tests')
-rw-r--r--tests/integration/test_gemma.py59
1 files changed, 59 insertions, 0 deletions
diff --git a/tests/integration/test_gemma.py b/tests/integration/test_gemma.py
index 676812d..d9ebeb1 100644
--- a/tests/integration/test_gemma.py
+++ b/tests/integration/test_gemma.py
@@ -1,10 +1,18 @@
"""Integration tests for gemma API endpoints"""
import unittest
+from dataclasses import dataclass
+from typing import Callable
from unittest import mock
from gn3.app import create_app
+@dataclass
+class MockRedis:
+ """Mock File object returned by request.files"""
+ redis: Callable
+
+
class GemmaAPITest(unittest.TestCase):
"""Test cases for the Gemma API"""
def setUp(self):
@@ -18,3 +26,54 @@ class GemmaAPITest(unittest.TestCase):
self.assertEqual(response.get_json(),
{"status": 0, "output": "v1.9"})
self.assertEqual(response.status_code, 200)
+
+ @mock.patch("gn3.api.gemma.redis.Redis")
+ @mock.patch("gn3.api.gemma.queue_cmd")
+ @mock.patch("gn3.api.gemma.generate_gemma_computation_cmd")
+ def test_run_gemma(self, mock_gemma_computation_cmd,
+ mock_queue_cmd, mock_redis):
+ """Test that gemma composes the command correctly"""
+ _redis_conn = MockRedis(redis=mock.MagicMock())
+ mock_redis.return_value = _redis_conn
+ mock_gemma_computation_cmd.side_effect = [
+ ("gemma-wrapper --json -- "
+ "-g genofile.txt -p "
+ "test.txt -a genofile_snps.txt "
+ "-gk > /tmp/gn2/"
+ "bxd_K_gUFhGu4rLG7k+CXLPk1OUg.txt"),
+ ("gemma-wrapper --json -- "
+ "-g genofile.txt -p "
+ "test.txt -a genofile_snps.txt "
+ "-gk > /tmp/gn2/"
+ "bxd_GWA_gUFhGu4rLG7k+CXLPk1OUg.txt")
+ ]
+ mock_queue_cmd.return_value = "my-unique-id"
+ response = self.app.post("/gemma/run", json={
+ "trait_filename": "BXD.txt",
+ "geno_filename": "BXD_geno",
+ "values": ["X", "N/A", "X"],
+ "dataset_groupname": "BXD",
+ "trait_name": "Height",
+ "email": "me@me.com",
+ "dataset_name": "BXD"
+ })
+ mock_queue_cmd.assert_has_calls(
+ [mock.call(conn=_redis_conn,
+ email="me@me.com",
+ cmd=("gemma-wrapper --json -- -g "
+ "genofile.txt -p test.txt "
+ "-a genofile_snps.txt -gk > "
+ "/tmp/gn2/bxd_K_gUFhGu4rLG7k+CXLPk1OUg.txt "
+ "&& gemma-wrapper --json -- -g "
+ "genofile.txt -p test.txt "
+ "-a genofile_snps.txt "
+ "-gk > "
+ "/tmp/gn2/"
+ "bxd_GWA_gUFhGu4rLG7k+CXLPk1OUg.txt"))]
+ )
+ # mock_pheno_txt_file.return_value = "/tmp/gn2/BXD_6OBEPW."
+ self.assertEqual(
+ response.get_json(),
+ {"unique_id": 'my-unique-id',
+ "status": "queued",
+ "output_file": "BXD_GWA_9lo8zwOOXbfB73EcyXxAYQ.txt"})