From f887baaf66cc157f0c77237c41e70e42fe03549c Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Fri, 12 Feb 2021 16:36:21 +0300 Subject: Add new procedure for composing a gemma cmd * gn3/commands.py: New file * tests/unit/test_commands.py: New test-cases for ^^. --- tests/unit/test_commands.py | 29 +++++++++++++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 tests/unit/test_commands.py (limited to 'tests/unit') diff --git a/tests/unit/test_commands.py b/tests/unit/test_commands.py new file mode 100644 index 0000000..a319332 --- /dev/null +++ b/tests/unit/test_commands.py @@ -0,0 +1,29 @@ +"""Test cases for procedures defined in commands.py""" +import os +import unittest + +from unittest import mock +from gn3.commands import compose_gemma_cmd + + +class TestCommands(unittest.TestCase): + """Test cases for commands.py""" + + @mock.patch("gn3.commands.lookup_file") + def test_compose_gemma_cmd_no_extra_args(self, mock_lookup_file): + """Test that thhe gemma cmd is composed correctly""" + metadata_file = os.path.join(os.path.dirname(__file__), + "test_data/metadata.json") + mock_lookup_file.side_effect = [metadata_file, + "/tmp/genofile.txt", + "/tmp/gf13Ad0tRX/phenofile.txt"] + self.assertEqual(compose_gemma_cmd("gf13Ad0t", + "metadata.json", + gemma_wrapper_cmd="gemma-wrapper", + gemma_wrapper_kwargs=None, + gemma_kwargs=None, + gemma_args=["-gk"]), + ("gemma-wrapper --json -- " + "-g /tmp/genofile.txt " + "-p /tmp/gf13Ad0tRX/phenofile.txt" + " -gk")) -- cgit v1.2.3