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authorBonfaceKilz2021-02-12 16:36:21 +0300
committerBonfaceKilz2021-02-12 21:13:30 +0300
commitf887baaf66cc157f0c77237c41e70e42fe03549c (patch)
tree0d1cc2c8b01f910f436906c109be7b26d9be4e04 /tests/unit
parentfcf6fbdaaae460bed917b73db033a3d063443389 (diff)
downloadgenenetwork3-f887baaf66cc157f0c77237c41e70e42fe03549c.tar.gz
Add new procedure for composing a gemma cmd
* gn3/commands.py: New file * tests/unit/test_commands.py: New test-cases for ^^.
Diffstat (limited to 'tests/unit')
-rw-r--r--tests/unit/test_commands.py29
1 files changed, 29 insertions, 0 deletions
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"))