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#!/usr/bin/python3
import os
import sys
import unittest
from unittest.mock import patch
sys.path.append(os.path.abspath(os.path.join(os.path.dirname(__file__), '..', 'scripts')))
import slurm_srst2
class TestSamtoolExec(unittest.TestCase):
@patch('slurm_srst2.sys.stdout')
@patch('slurm_srst2.check_command_versions')
@patch('slurm_srst2.run_command')
@patch('slurm_srst2.os.path')
@patch('slurm_srst2.os.environ')
def test_samtools_index_with_overide(self, env_mock, path_mock, run_mock,
version_mock, stdout_mock):
path_mock.exists.return_value = False
path_mock.isfile.side_effect = lambda f: 'missing' not in f
env_mock.get.side_effect = {'SRST2_SAMTOOLS': '/usr/bin/samtools'}.get
slurm_srst2.samtools_index(['foo'])
self.assertEqual(version_mock.call_count, 1)
self.assertEqual(version_mock.call_args[0][0], ['/usr/bin/samtools'])
self.assertEqual(run_mock.call_count, 1)
run_mock.assert_called_once_with(['/usr/bin/samtools', 'faidx',
'foo'])
@patch('slurm_srst2.sys.stdout')
@patch('slurm_srst2.check_command_versions')
@patch('slurm_srst2.run_command')
@patch('slurm_srst2.os.path')
@patch('slurm_srst2.os.environ')
def test_samtools_index_with_default(self, env_mock, path_mock, run_mock,
version_mock, stdout_mock):
path_mock.exists.return_value = False
env_mock.get.return_value = None
slurm_srst2.samtools_index(['foo'])
self.assertEqual(version_mock.call_count, 1)
self.assertEqual(version_mock.call_args[0][0], ['samtools'])
self.assertEqual(run_mock.call_count, 1)
run_mock.assert_called_once_with(['samtools', 'faidx',
'foo'])
@patch('slurm_srst2.sys.stdout')
@patch('slurm_srst2.check_command_versions')
@patch('slurm_srst2.run_command')
@patch('slurm_srst2.os.path')
@patch('slurm_srst2.os.environ')
def test_samtools_index_with_missing_overide(self, env_mock, path_mock,
run_mock, version_mock,
stdout_mock):
path_mock.exists.return_value = False
path_mock.isfile.side_effect = lambda f: 'missing' not in f
env_mock.get.side_effect = {'SRST2_SAMTOOLS': '/missing/samtools'}.get
slurm_srst2.samtools_index(['foo'])
self.assertEqual(version_mock.call_count, 1)
self.assertEqual(version_mock.call_args[0][0], ['samtools'])
self.assertEqual(run_mock.call_count, 1)
run_mock.assert_called_once_with(['samtools', 'faidx',
'foo'])
class TestBowtieIndex(unittest.TestCase):
@patch('slurm_srst2.sys.stdout')
@patch('slurm_srst2.check_command_versions')
@patch('slurm_srst2.run_command')
@patch('slurm_srst2.os.path')
@patch('slurm_srst2.os.environ')
def test_bowtie_index_with_overides(self, env_mock, path_mock, run_mock,
version_mock, stdout_mock):
path_mock.exists.return_value = False
path_mock.isfile.side_effect = lambda f: 'missing' not in f
fake_env_variables = {'SRST2_BOWTIE2': '/usr/bin/bowtie2',
'SRST2_BOWTIE2_BUILD': '/usr/bin/bowtie2-build'}
env_mock.get.side_effect = fake_env_variables.get
slurm_srst2.bowtie_index(['foo'])
self.assertEqual(version_mock.call_count, 1)
self.assertEqual(version_mock.call_args[0][0], ['/usr/bin/bowtie2',
'--version'])
self.assertEqual(run_mock.call_count, 1)
run_mock.assert_called_once_with(['/usr/bin/bowtie2-build', 'foo', 'foo'])
@patch('slurm_srst2.sys.stdout')
@patch('slurm_srst2.check_command_versions')
@patch('slurm_srst2.run_command')
@patch('slurm_srst2.os.path')
@patch('slurm_srst2.os.environ')
def test_bowtie_index_with_partial_overide(self, env_mock, path_mock, run_mock,
version_mock, stdout_mock):
path_mock.exists.return_value = False
path_mock.isfile.side_effect = lambda f: 'missing' not in f
fake_env_variables = {'SRST2_BOWTIE2': '/usr/bin/bowtie2'}
env_mock.get.side_effect = fake_env_variables.get
slurm_srst2.bowtie_index(['foo'])
self.assertEqual(version_mock.call_count, 1)
self.assertEqual(version_mock.call_args[0][0], ['/usr/bin/bowtie2',
'--version'])
self.assertEqual(run_mock.call_count, 1)
run_mock.assert_called_once_with(['/usr/bin/bowtie2-build', 'foo', 'foo'])
@patch('slurm_srst2.sys.stdout')
@patch('slurm_srst2.check_command_versions')
@patch('slurm_srst2.run_command')
@patch('slurm_srst2.os.path')
@patch('slurm_srst2.os.environ')
def test_bowtie_index_with_other_overide(self, env_mock, path_mock, run_mock,
version_mock, stdout_mock):
path_mock.exists.return_value = False
path_mock.isfile.side_effect = lambda f: 'missing' not in f
fake_env_variables = {'SRST2_BOWTIE2_BUILD': '/usr/bin/bowtie2-build'}
env_mock.get.side_effect = fake_env_variables.get
slurm_srst2.bowtie_index(['foo'])
self.assertEqual(version_mock.call_count, 1)
self.assertEqual(version_mock.call_args[0][0], ['bowtie2',
'--version'])
self.assertEqual(run_mock.call_count, 1)
run_mock.assert_called_once_with(['/usr/bin/bowtie2-build', 'foo', 'foo'])
@patch('slurm_srst2.sys.stdout')
@patch('slurm_srst2.check_command_versions')
@patch('slurm_srst2.run_command')
@patch('slurm_srst2.os.path')
@patch('slurm_srst2.os.environ')
def test_bowtie_index_with_default(self, env_mock, path_mock, run_mock,
version_mock, stdout_mock):
path_mock.exists.return_value = False
env_mock.get.return_value = None
slurm_srst2.bowtie_index(['foo'])
self.assertEqual(version_mock.call_count, 1)
self.assertEqual(version_mock.call_args[0][0], ['bowtie2',
'--version'])
self.assertEqual(run_mock.call_count, 1)
run_mock.assert_called_once_with(['bowtie2-build', 'foo', 'foo'])
@patch('slurm_srst2.sys.stdout')
@patch('slurm_srst2.check_command_versions')
@patch('slurm_srst2.run_command')
@patch('slurm_srst2.os.path')
@patch('slurm_srst2.os.environ')
def test_bowtie_index_with_missing_overide(self, env_mock, path_mock,
run_mock, version_mock,
stdout_mock):
path_mock.exists.return_value = False
path_mock.isfile.side_effect = lambda f: 'missing' not in f
env_mock.get.side_effect = {'SRST2_SAMTOOLS': '/missing/bowtie'}.get
slurm_srst2.bowtie_index(['foo'])
self.assertEqual(version_mock.call_count, 1)
self.assertEqual(version_mock.call_args[0][0], ['bowtie2',
'--version'])
self.assertEqual(run_mock.call_count, 1)
run_mock.assert_called_once_with(['bowtie2-build', 'foo', 'foo'])
@patch('slurm_srst2.sys.stdout')
@patch('slurm_srst2.check_command_versions')
@patch('slurm_srst2.run_command')
@patch('slurm_srst2.os.path')
@patch('slurm_srst2.os.environ')
def test_bowtie_index_with_one_missing_overide(self, env_mock, path_mock,
run_mock, version_mock,
stdout_mock):
path_mock.exists.return_value = False
path_mock.isfile.side_effect = lambda f: 'missing' not in f
fake_env_variables = {'SRST2_BOWTIE2': '/missing/bowtie2',
'SRST2_BOWTIE2_BUILD': '/usr/bin/bowtie2-build'}
env_mock.get.side_effect = fake_env_variables.get
slurm_srst2.bowtie_index(['foo'])
self.assertEqual(version_mock.call_count, 1)
self.assertEqual(version_mock.call_args[0][0], ['bowtie2',
'--version'])
self.assertEqual(run_mock.call_count, 1)
run_mock.assert_called_once_with(['/usr/bin/bowtie2-build', 'foo', 'foo'])
@patch('slurm_srst2.sys.stdout')
@patch('slurm_srst2.check_command_versions')
@patch('slurm_srst2.run_command')
@patch('slurm_srst2.os.path')
@patch('slurm_srst2.os.environ')
def test_bowtie_index_with_other_missing_overide(self, env_mock, path_mock,
run_mock, version_mock,
stdout_mock):
path_mock.exists.return_value = False
path_mock.isfile.side_effect = lambda f: 'missing' not in f
fake_env_variables = {'SRST2_BOWTIE2': '/usr/bin/bowtie2',
'SRST2_BOWTIE2_BUILD': '/missing/bowtie2-build'}
env_mock.get.side_effect = fake_env_variables.get
slurm_srst2.bowtie_index(['foo'])
self.assertEqual(version_mock.call_count, 1)
self.assertEqual(version_mock.call_args[0][0], ['/usr/bin/bowtie2',
'--version'])
self.assertEqual(run_mock.call_count, 1)
run_mock.assert_called_once_with(['/usr/bin/bowtie2-build', 'foo', 'foo'])
@patch('slurm_srst2.sys.stdout')
@patch('slurm_srst2.check_command_versions')
@patch('slurm_srst2.run_command')
@patch('slurm_srst2.os.path')
@patch('slurm_srst2.os.environ')
def test_bowtie_index_with_missing_inference(self, env_mock, path_mock,
run_mock, version_mock,
stdout_mock):
path_mock.exists.return_value = False
path_mock.isfile.side_effect = lambda f: f == '/usr/bin/bowtie2'
fake_env_variables = {'SRST2_BOWTIE2': '/usr/bin/bowtie2'}
env_mock.get.side_effect = fake_env_variables.get
slurm_srst2.bowtie_index(['foo'])
self.assertEqual(version_mock.call_count, 1)
self.assertEqual(version_mock.call_args[0][0], ['/usr/bin/bowtie2',
'--version'])
self.assertEqual(run_mock.call_count, 1)
run_mock.assert_called_once_with(['bowtie2-build', 'foo', 'foo'])
if __name__ == '__main__':
unittest.main()
|
