Add new endpoint

"/gwa-compute/<k_filename>/loco/covariates/maf/<maf>/<token>"

1 files changed, 48 insertions, 1 deletions

diff --git a/tests/integration/test_gemma.py b/tests/integration/test_gemma.py
index 61421f2..6d2116b 100644
--- a/tests/integration/test_gemma.py
+++ b/tests/integration/test_gemma.py
@@ -324,7 +324,6 @@ class GemmaAPITest(unittest.TestCase):
             "geno": "genofile.txt",
             "pheno": "phenofile.txt",
             "snps": "snpfile.txt",
-            "covar": "covarfile.txt",
         }
         mock_hash.return_value = "hash"
         response = self.app.post(("/api/gemma/gwa-compute/"
@@ -349,3 +348,51 @@ class GemmaAPITest(unittest.TestCase):
             "status": "queued",
             "output_file": "hash-gwa-output.json"
         })
+
+    @mock.patch("gn3.api.gemma.queue_cmd")
+    @mock.patch("gn3.api.gemma.get_hash_of_files")
+    @mock.patch("gn3.api.gemma.jsonfile_to_dict")
+    @mock.patch("gn3.api.gemma.do_paths_exist")
+    @mock.patch("gn3.api.gemma.redis.Redis")
+    def test_gwa_compute_with_loco_covars(self, mock_redis,
+                                          mock_path_exist,
+                                          mock_json, mock_hash,
+                                          mock_queue_cmd):
+        """Test /gemma/gwa-compute/<k-inputfile>/loco/covariates/maf/<maf><token>
+
+        """
+        mock_path_exist.return_value, _redis_conn = True, mock.MagicMock()
+        mock_redis.return_value = _redis_conn
+        mock_queue_cmd.return_value = "my-unique-id"
+        mock_json.return_value = {
+            "geno": "genofile.txt",
+            "pheno": "phenofile.txt",
+            "snps": "snpfile.txt",
+            "covar": "covarfile.txt",
+        }
+        mock_hash.return_value = "hash"
+        response = self.app.post(("/api/gemma/gwa-compute/"
+                                  "hash-k-output.json/loco/"
+                                  "covariates/maf/21/my-token"))
+        mock_hash.assert_called_once_with(['/tmp/my-token/genofile.txt',
+                                           '/tmp/my-token/phenofile.txt',
+                                           '/tmp/my-token/snpfile.txt',
+                                           "/tmp/my-token/covarfile.txt"
+                                           ])
+        mock_queue_cmd.assert_called_once_with(
+            conn=_redis_conn,
+            email=None,
+            job_queue='GN3::job-queue',
+            cmd=("gemma-wrapper --json --loco --input "
+                 "/tmp/my-token/hash-k-output.json -- "
+                 "-g /tmp/my-token/genofile.txt "
+                 "-p /tmp/my-token/phenofile.txt "
+                 "-a /tmp/my-token/snpfile.txt "
+                 "-c /tmp/my-token/covarfile.txt "
+                 "-lmm 9 -maf 21.0 "
+                 "-gk > /tmp/my-token/hash-gwa-output.json"))
+        self.assertEqual(response.get_json(), {
+            "unique_id": "my-unique-id",
+            "status": "queued",
+            "output_file": "hash-gwa-output.json"
+        })