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"""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"))
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