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-rw-r--r--gn3/commands.py6
-rw-r--r--tests/unit/test_commands.py17
2 files changed, 20 insertions, 3 deletions
diff --git a/gn3/commands.py b/gn3/commands.py
index 7a4eb48..7287348 100644
--- a/gn3/commands.py
+++ b/gn3/commands.py
@@ -20,9 +20,9 @@ def compose_gemma_cmd(
"""Compose a valid GEMMA command given the correct values"""
cmd = f"{gemma_wrapper_cmd} --json"
if gemma_wrapper_kwargs:
- cmd += (" " # Add extra space between commands
- " ".join([f"--{key} {val}" for key, val
- in gemma_wrapper_kwargs.items()]))
+ cmd += " " # Add extra space between commands
+ cmd += " ".join([f"--{key} {val}" for key, val
+ in gemma_wrapper_kwargs.items()])
cmd += " -- "
if gemma_kwargs:
cmd += " ".join([f"-{key} {val}"
diff --git a/tests/unit/test_commands.py b/tests/unit/test_commands.py
index 846d20c..c51118d 100644
--- a/tests/unit/test_commands.py
+++ b/tests/unit/test_commands.py
@@ -36,6 +36,23 @@ class TestCommands(unittest.TestCase):
"-p /tmp/gf13Ad0tRX/phenofile.txt"
" -gk"))
+ def test_compose_gemma_cmd_extra_args(self):
+ """Test that the gemma cmd is composed correctly"""
+ self.assertEqual(
+ compose_gemma_cmd(gemma_wrapper_cmd="gemma-wrapper",
+ gemma_wrapper_kwargs={
+ "loco": "1,2,3,4"
+ },
+ gemma_kwargs={
+ "g": "/tmp/genofile.txt",
+ "p": "/tmp/gf13Ad0tRX/phenofile.txt"
+ },
+ gemma_args=["-gk"]),
+ ("gemma-wrapper --json --loco 1,2,3,4 -- "
+ "-g /tmp/genofile.txt "
+ "-p /tmp/gf13Ad0tRX/phenofile.txt"
+ " -gk"))
+
def test_queue_cmd_exception_raised_when_redis_is_down(self):
"""Test that the correct error is raised when Redis is unavailable"""
self.assertRaises(RedisConnectionError,