Remove "/k-gwa-computation"

2 files changed, 0 insertions, 167 deletions

diff --git a/gn3/api/gemma.py b/gn3/api/gemma.py
index ed698d3..21c4cf5 100644
--- a/gn3/api/gemma.py
+++ b/gn3/api/gemma.py
@@ -26,64 +26,6 @@ def get_version():
     return jsonify(run_cmd(f"{gemma_cmd} -v | head -n 1"))
 
 
-# This is basically extracted from genenetwork2
-# wqflask/wqflask/marker_regression/gemma_ampping.py
-@gemma.route("/k-gwa-computation", methods=["POST"])
-def run_gemma():
-    """Generates a command for generating K-Values and then later, generate a GWA
-command that contains markers. These commands are queued; and the expected
-file output is returned.
-
-    """
-    data = request.get_json()
-    app_defaults = current_app.config
-    __hash = generate_hash_of_string(f"{data.get('genofile_name')}_"
-                                     ''.join(data.get("values", "")))
-    gemma_kwargs = {
-        "geno_filename":
-        os.path.join(app_defaults.get("GENODIR"), "bimbam",
-                     f"{data.get('geno_filename')}"),
-        "trait_filename":
-        generate_pheno_txt_file(
-            tmpdir=app_defaults.get("TMPDIR"),
-            values=data.get("values"),
-            # Generate this file on the fly!
-            trait_filename=(f"{data.get('dataset_groupname')}_"
-                            f"{data.get('trait_name')}_"
-                            f"{__hash}.txt"))
-    }
-    gemma_wrapper_kwargs = {}
-    if data.get("loco"):
-        gemma_wrapper_kwargs["loco"] = f"--input {data.get('loco')}"
-    k_computation_cmd = generate_gemma_computation_cmd(
-        gemma_cmd=app_defaults.get("GEMMA_WRAPPER_CMD"),
-        gemma_wrapper_kwargs={"loco": f"--input {data.get('loco')}"},
-        gemma_kwargs=gemma_kwargs,
-        output_file=(f"{app_defaults.get('TMPDIR')}/gn2/"
-                     f"{data.get('dataset_name')}_K_"
-                     f"{__hash}.json"))
-    gemma_kwargs["lmm"] = data.get("lmm", 9)
-    gemma_wrapper_kwargs["input"] = (f"{data.get('dataset_name')}_K_"
-                                     f"{__hash}.json")
-    gwa_cmd = generate_gemma_computation_cmd(
-        gemma_wrapper_kwargs=gemma_wrapper_kwargs,
-        gemma_cmd=app_defaults.get("GEMMA_WRAPPER_CMD"),
-        gemma_kwargs=gemma_kwargs,
-        output_file=(f"{data.get('dataset_name')}_GWA_"
-                     f"{__hash}.txt"))
-    if not all([k_computation_cmd, gwa_cmd]):
-        return jsonify(status=128,
-                       error="Unable to generate cmds for computation!"), 500
-    return jsonify(unique_id=queue_cmd(
-        conn=redis.Redis(),
-        email=data.get("email"),
-        job_queue=app_defaults.get("REDIS_JOB_QUEUE"),
-        cmd=f"{k_computation_cmd} && {gwa_cmd}"),
-                   status="queued",
-                   output_file=(f"{data.get('dataset_name')}_GWA_"
-                                f"{__hash}.txt"))
-
-
 @gemma.route("/status/<unique_id>", methods=["GET"])
 def check_cmd_status(unique_id):
     """Given a (url-encoded) UNIQUE-ID which is returned when hitting any of the
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
@@ -39,115 +39,6 @@ class GemmaAPITest(unittest.TestCase):
         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"""
         mock_hget = mock.MagicMock()