def setUp(self):
self.empty_args = Namespace()
self.af = ArgFiller(self.empty_args)
pass
def setUp(self):
self.empty_args = Namespace()
self.af = ArgFiller(self.empty_args)
pass
class ArgFillerTest(unittest.TestCase):
"""Tests for functions and classes in rnaseqflow.cliutils
Long docstring for testing
"""
FIXTURES = os.path.join(os.path.dirname(__file__), "fixtures")
ADAPTER_FILE = os.path.join(FIXTURES, "test_adapters.fasta")
def setUp(self):
self.empty_args = Namespace()
self.af = ArgFiller(self.empty_args)
pass
def tearDown(self):
pass
def test_fill_root(self):
with mock.patch("__builtin__.raw_input", return_value=self.FIXTURES):
self.af.fill(["root"])
self.assertEqual(self.empty_args.root, self.FIXTURES)
with mock.patch("__builtin__.raw_input", return_value="junk"):
self.af.fill(["root"])
self.assertEqual(self.empty_args.root, self.FIXTURES)
def test_fill_ext(self):
with mock.patch("__builtin__.raw_input", return_value=".fastq"):
self.af.fill(["ext"])
self.assertEqual(self.empty_args.ext, ".fastq")
with mock.patch("__builtin__.raw_input", return_value="junk"):
self.af.fill(["ext"])
self.assertEqual(self.empty_args.ext, ".fastq")
def test_fill_blocksize(self):
with mock.patch("__builtin__.raw_input", return_value="100"):
self.af.fill(["blocksize"])
self.assertEqual(self.empty_args.blocksize, 100)
with mock.patch("__builtin__.raw_input", return_value="junk"):
self.af.fill(["blocksize"])
self.assertEqual(self.empty_args.blocksize, 100)
def test_fill_adapters(self):
with mock.patch("__builtin__.raw_input", return_value=self.ADAPTER_FILE):
self.af.fill(["adapters"])
self.assertEqual(self.empty_args.adapters, self.ADAPTER_FILE)
with mock.patch("__builtin__.raw_input", return_value="junk"):
self.af.fill(["adapters"])
self.assertEqual(self.empty_args.adapters, self.ADAPTER_FILE)
def test_fill_fastq_args(self):
with mock.patch("__builtin__.raw_input", return_value="-q 30"):
self.af.fill(["fastq_args"])
self.assertEqual(self.empty_args.fastq_args, "-q 30")
with mock.patch("__builtin__.raw_input", return_value="junk"):
self.af.fill(["fastq_args"])
self.assertEqual(self.empty_args.fastq_args, "-q 30")
def test_fill_quiet(self):
self.af.fill(["quiet"])
self.assertFalse(self.empty_args.quiet)
self.empty_args.quiet = True
self.af.fill(["quiet"])
self.assertTrue(self.empty_args.quiet)
def test_trim(self):
correct_docstring = "Tests for functions and classes in " "rnaseqflow.cliutils\n\n" "Long docstring for testing"
self.assertEqual(trim(self.__doc__), correct_docstring)
self.assertEqual(trim(None), "")
def test_firstline(self):
correct_firstline = "Tests for functions and classes in rnaseqflow.cliutils"
self.assertEqual(firstline(self.__doc__), correct_firstline)
self.assertEqual(firstline(None), "")
def test_all_subclasses(self):
class Base(object):
pass
self.assertListEqual(all_subclasses(Base), [])
class Inherited1(Base):
pass
self.assertListEqual(all_subclasses(Base), [Inherited1])
class Inherited2(Base):
pass
self.assertListEqual(all_subclasses(Base), [Inherited1, Inherited2])
class ArgFillerTest(unittest.TestCase):
"""Tests for functions and classes in rnaseqflow.cliutils
Long docstring for testing
"""
FIXTURES = os.path.join(os.path.dirname(__file__), 'fixtures')
ADAPTER_FILE = os.path.join(FIXTURES, 'test_adapters.fasta')
def setUp(self):
self.empty_args = Namespace()
self.af = ArgFiller(self.empty_args)
pass
def tearDown(self):
pass
def test_fill_root(self):
with mock.patch('__builtin__.raw_input', return_value=self.FIXTURES):
self.af.fill(['root'])
self.assertEqual(self.empty_args.root, self.FIXTURES)
with mock.patch('__builtin__.raw_input', return_value='junk'):
self.af.fill(['root'])
self.assertEqual(self.empty_args.root, self.FIXTURES)
def test_fill_ext(self):
with mock.patch('__builtin__.raw_input', return_value='.fastq'):
self.af.fill(['ext'])
self.assertEqual(self.empty_args.ext, '.fastq')
with mock.patch('__builtin__.raw_input', return_value='junk'):
self.af.fill(['ext'])
self.assertEqual(self.empty_args.ext, '.fastq')
def test_fill_blocksize(self):
with mock.patch('__builtin__.raw_input', return_value='100'):
self.af.fill(['blocksize'])
self.assertEqual(self.empty_args.blocksize, 100)
with mock.patch('__builtin__.raw_input', return_value='junk'):
self.af.fill(['blocksize'])
self.assertEqual(self.empty_args.blocksize, 100)
def test_fill_adapters(self):
with mock.patch('__builtin__.raw_input',
return_value=self.ADAPTER_FILE):
self.af.fill(['adapters'])
self.assertEqual(self.empty_args.adapters, self.ADAPTER_FILE)
with mock.patch('__builtin__.raw_input', return_value='junk'):
self.af.fill(['adapters'])
self.assertEqual(self.empty_args.adapters, self.ADAPTER_FILE)
def test_fill_fastq_args(self):
with mock.patch('__builtin__.raw_input', return_value='-q 30'):
self.af.fill(['fastq_args'])
self.assertEqual(self.empty_args.fastq_args, '-q 30')
with mock.patch('__builtin__.raw_input', return_value='junk'):
self.af.fill(['fastq_args'])
self.assertEqual(self.empty_args.fastq_args, '-q 30')
def test_fill_quiet(self):
self.af.fill(['quiet'])
self.assertFalse(self.empty_args.quiet)
self.empty_args.quiet = True
self.af.fill(['quiet'])
self.assertTrue(self.empty_args.quiet)
def test_trim(self):
correct_docstring = "Tests for functions and classes in " \
"rnaseqflow.cliutils\n\n" \
"Long docstring for testing"
self.assertEqual(trim(self.__doc__), correct_docstring)
self.assertEqual(trim(None), '')
def test_firstline(self):
correct_firstline = "Tests for functions and classes in rnaseqflow.cliutils"
self.assertEqual(firstline(self.__doc__), correct_firstline)
self.assertEqual(firstline(None), '')
def test_all_subclasses(self):
class Base(object):
pass
self.assertListEqual(all_subclasses(Base), [])
class Inherited1(Base):
pass
self.assertListEqual(all_subclasses(Base), [Inherited1])
class Inherited2(Base):
pass
self.assertListEqual(all_subclasses(Base), [Inherited1, Inherited2])