From 776598729bcff12bea933ff7cb4864e1c3eea0c8 Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Mon, 8 Mar 2021 15:26:33 +0300
Subject: Delete "generate_gemma_computation_cmd"

---
 gn3/computations/gemma.py             | 22 ----------------------
 tests/unit/computations/test_gemma.py | 21 ---------------------
 2 files changed, 43 deletions(-)

diff --git a/gn3/computations/gemma.py b/gn3/computations/gemma.py
index 3c6bd29..bf8b151 100644
--- a/gn3/computations/gemma.py
+++ b/gn3/computations/gemma.py
@@ -49,28 +49,6 @@ def do_paths_exist(paths: ValuesView) -> bool:
     return True
 
 
-def generate_gemma_computation_cmd(
-        gemma_cmd: str, gemma_kwargs: Dict[str, str], output_file: str,
-        gemma_wrapper_kwargs: Dict[str, str]) -> Optional[str]:
-    """Create a computation cmd"""
-    geno_filename = gemma_kwargs.get("geno_filename", "")
-    trait_filename = gemma_kwargs.get("trait_filename")
-    ext, snps_filename = geno_filename.partition(".")[-1], ""
-    if geno_filename:
-        snps_filename = geno_filename.replace(f".{ext}", "")
-        snps_filename += f"_snps.{ext}"
-    _kwargs = {"g": geno_filename, "p": trait_filename}
-    _kwargs["a"] = snps_filename
-    if not do_paths_exist(_kwargs.values()):  # Prevents injection!
-        return None
-    if _kwargs.get("lmm"):
-        _kwargs["lmm"] = gemma_kwargs.get("lmm")
-    return compose_gemma_cmd(gemma_wrapper_cmd=gemma_cmd,
-                             gemma_wrapper_kwargs=gemma_wrapper_kwargs,
-                             gemma_kwargs=_kwargs,
-                             gemma_args=["-gk", ">", output_file])
-
-
 # pylint: disable=R0913
 def generate_gemma_cmd(gemma_cmd: str,
                        output_dir: str,
diff --git a/tests/unit/computations/test_gemma.py b/tests/unit/computations/test_gemma.py
index 4a76bef..f3b31e5 100644
--- a/tests/unit/computations/test_gemma.py
+++ b/tests/unit/computations/test_gemma.py
@@ -5,7 +5,6 @@ from unittest import mock
 from gn3.computations.gemma import generate_gemma_cmd
 from gn3.computations.gemma import generate_hash_of_string
 from gn3.computations.gemma import generate_pheno_txt_file
-from gn3.computations.gemma import generate_gemma_computation_cmd
 
 
 class TestGemma(unittest.TestCase):
@@ -32,26 +31,6 @@ class TestGemma(unittest.TestCase):
         self.assertEqual(generate_hash_of_string("I^iQP&TlSR^z"),
                          "hMVRw8kbEp49rOmoIkhMjA")
 
-    @mock.patch("gn3.computations.gemma.do_paths_exist")
-    def test_compose_k_computation_cmd(self, mock_pathsp):
-        """Test that a K computation cmd is constructed properly"""
-        mock_pathsp.return_value = True
-        self.assertEqual(
-            generate_gemma_computation_cmd(
-                gemma_cmd="gemma-wrapper",
-                gemma_wrapper_kwargs=None,
-                gemma_kwargs={
-                    "geno_filename": "genofile.txt",
-                    "trait_filename": "test.txt",
-                    "covar_filename": "genofile_snps.txt"
-                },
-                output_file="/tmp/gn2/k_output_gUFhGu4rLG7k+CXLPk1OUg.txt",
-            ), ("gemma-wrapper --json -- "
-                "-g genofile.txt -p "
-                "test.txt -a genofile_snps.txt "
-                "-gk > /tmp/gn2/"
-                "k_output_gUFhGu4rLG7k+CXLPk1OUg.txt"))
-
     @mock.patch("gn3.computations.gemma.get_hash_of_files")
     def test_compute_k_values_without_loco(self, mock_get_hash):
         """Test computing k valuse without loco"""
-- 
cgit v1.2.3