Add tests for "/gemma/run" endpoint

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"})