diff options
Diffstat (limited to 'tests/unit')
| -rw-r--r-- | tests/unit/computations/test_rqtl.py | 41 | ||||
| -rw-r--r-- | tests/unit/test_commands.py | 26 |
2 files changed, 67 insertions, 0 deletions
diff --git a/tests/unit/computations/test_rqtl.py b/tests/unit/computations/test_rqtl.py new file mode 100644 index 0000000..b16f136 --- /dev/null +++ b/tests/unit/computations/test_rqtl.py @@ -0,0 +1,41 @@ +"""Test cases for procedures defined in computations.rqtl"""
+import unittest
+
+from unittest import mock
+from gn3.computations.rqtl import generate_rqtl_cmd
+
+class TestRqtl(unittest.TestCase):
+ """Test cases for computations.rqtl module"""
+ @mock.patch("gn3.computations.rqtl.generate_hash_of_string")
+ @mock.patch("gn3.computations.rqtl.get_hash_of_files")
+ def test_generate_rqtl_command(self, mock_get_hash_files, mock_generate_hash_string):
+ """Test computing mapping results with R/qtl"""
+ mock_get_hash_files.return_value = "my-hash1"
+ mock_generate_hash_string.return_value = "my-hash2"
+
+ self.assertEqual(
+ generate_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"
+ ]), {
+ "output_file":
+ "my-hash1my-hash2my-hash2-output.json",
+ "rqtl_cmd": (
+ "rqtl-wrapper "
+ "--g genofile --p phenofile "
+ "--model normal --method hk "
+ "--nperm 1000 --scale Mb "
+ "--control rs123456 "
+ "--addcovar --interval"
+ )
+ })
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, |