From e5bcb0faccf67f213538cad3670a8d1378c56ce7 Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Mon, 8 Mar 2021 15:22:26 +0300
Subject: Remove "/k-gwa-computation"

---
 tests/integration/test_gemma.py | 109 ----------------------------------------
 1 file changed, 109 deletions(-)

(limited to 'tests/integration')

diff --git a/tests/integration/test_gemma.py b/tests/integration/test_gemma.py
index bfce37a..7a7f520 100644
--- a/tests/integration/test_gemma.py
+++ b/tests/integration/test_gemma.py
@@ -38,115 +38,6 @@ 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_no_loco(self, mock_gemma_computation_cmd,
-                               mock_queue_cmd, mock_redis):
-        """Test that gemma composes the command correctly without loco"""
-        _redis_conn = MockRedis(redis=mock.MagicMock(), hget=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 --input /tmp/gn2/"
-             "bxd_K_gUFhGu4rLG7k+CXLPk1OUg.txt -- "
-             "-a genofile_snps.txt -lmm 9 "
-             "-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("/api/gemma/k-gwa-computation",
-                                 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",
-                      job_queue="GN3::job-queue",
-                      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 --input "
-                           "/tmp/gn2/bxd_K_gUFhGu4rLG7k+CXLPk1OUg.txt"
-                           " -- -a genofile_snps.txt -lmm 9 -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_WzxVcfhKAn4fJnSWpsBq0g.txt"
-            })
-
-    @mock.patch("gn3.api.gemma.redis.Redis")
-    @mock.patch("gn3.api.gemma.queue_cmd")
-    def test_run_gemma_with_loco(self, mock_queue_cmd, mock_redis):
-        """Test that gemma composes the command correctly with loco"""
-        _redis_conn = MockRedis(redis=mock.MagicMock(), hget=mock.MagicMock())
-        mock_redis.return_value = _redis_conn
-        mock_queue_cmd.return_value = "my-unique-id"
-        response = self.app.post("/api/gemma/k-gwa-computation",
-                                 json={
-                                     "trait_filename":
-                                     os.path.abspath(
-                                         os.path.join(
-                                             os.path.dirname(__file__),
-                                             "test_data/")),
-                                     "geno_filename":
-                                     "BXD_geno.txt.gz",
-                                     "values": ["X", "N/A", "X"],
-                                     "dataset_groupname":
-                                     "BXD",
-                                     "trait_name":
-                                     "Height",
-                                     "email":
-                                     "me@me.com",
-                                     "dataset_name":
-                                     "BXD",
-                                     "loco":
-                                     "1,2,3,4,5,6"
-                                 })
-        mock_queue_cmd.called_with(
-            conn=_redis_conn,
-            email="me@me.com",
-            job_queue="GN3::job-queue",
-            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 --input "
-                 "/tmp/gn2/bxd_K_gUFhGu4rLG7k+CXLPk1OUg.txt"
-                 " -- -a genofile_snps.txt -lmm 9 -g "
-                 "genofile.txt -p test.txt "
-                 "-a genofile_snps.txt "
-                 "-gk > "
-                 "/tmp/gn2/"
-                 "bxd_GWA_gUFhGu4rLG7k+CXLPk1OUg.txt"))
-        self.assertEqual(
-            response.get_json(), {
-                "unique_id": 'my-unique-id',
-                "status": "queued",
-                "output_file": "BXD_GWA_WzxVcfhKAn4fJnSWpsBq0g.txt"
-            })
-
     @mock.patch("gn3.api.gemma.redis.Redis")
     def test_check_cmd_status(self, mock_redis):
         """Test that you can check the status of a given command"""
-- 
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