From d66b71a1e149ccddbbcc66e439067250827e0b6f Mon Sep 17 00:00:00 2001 From: zsloan Date: Tue, 18 May 2021 20:06:57 +0000 Subject: Added test for compose_rqtl_cmd in tests/unit/test_commands.py --- tests/unit/test_commands.py | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) diff --git a/tests/unit/test_commands.py b/tests/unit/test_commands.py index aafb3a2..a3d0273 100644 --- a/tests/unit/test_commands.py +++ b/tests/unit/test_commands.py @@ -6,6 +6,7 @@ from datetime import datetime from typing import Callable from unittest import mock from gn3.commands import compose_gemma_cmd +from gn3.commands import compose_rqtl_cmd from gn3.commands import queue_cmd from gn3.commands import run_cmd from gn3.exceptions import RedisConnectionError @@ -53,6 +54,31 @@ class TestCommands(unittest.TestCase): "-p /tmp/gf13Ad0tRX/phenofile.txt" " -gk")) + def test_compose_rqtl_cmd(self): + """Test that the R/qtl cmd is composed correctly""" + self.assertEqual( + compose_rqtl_cmd(rqtl_wrapper_cmd="rqtl-wrapper", + rqtl_wrapper_kwargs={ + "g": "genofile", + "p": "phenofile", + "model": "normal", + "method": "hk", + "nperm": 1000, + "scale": "Mb", + "control": "rs123456" + }, + rqtl_wrapper_bool_kwargs=[ + "addcovar", + "interval" + ]), + ("rqtl-wrapper " + "--g genofile --p phenofile " + "--model normal --method hk " + "--nperm 1000 --scale Mb " + "--control rs123456 " + "--addcovar --interval") + ) + 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, -- cgit v1.2.3