def test_run_no_files_from_hidef(self):
temp_dir = tempfile.mkdtemp()
try:
input_file = os.path.join(TestCdhidef.HUNDRED_NODE_DIR,
'input.txt')
f_out = io.StringIO()
f_err = io.StringIO()
fakecmd = os.path.join(temp_dir, 'foo.py')
write_fake_hidef(fakecmd, 'stdout',
'stderr',
temp_dir, 0)
myargs = [input_file, '--tempdir', temp_dir,
'--hidefcmd', fakecmd]
theargs = cdhidefcmd._parse_arguments('desc', myargs)
res = cdhidefcmd.run_hidef(theargs, out_stream=f_out,
err_stream=f_err)
err_data = f_err.getvalue()
out_data = f_out.getvalue()
self.assertEqual(0, len(out_data))
self.assertTrue('Output from cmd: ' in err_data)
self.assertEqual(5, res)
finally:
shutil.rmtree(temp_dir)
def test_run_hidef_success(self):
temp_dir = tempfile.mkdtemp()
try:
input_file = os.path.join(TestCdhidef.HUNDRED_NODE_DIR,
'input.txt')
f_out = io.StringIO()
f_err = io.StringIO()
fakecmd = os.path.join(temp_dir, 'foo.py')
write_fake_hidef(fakecmd, 'stdout',
'stderr',
TestCdhidef.HUNDRED_NODE_DIR, 0)
myargs = [input_file, '--tempdir', temp_dir,
'--hidefcmd', fakecmd]
theargs = cdhidefcmd._parse_arguments('desc', myargs)
res = cdhidefcmd.run_hidef(theargs, out_stream=f_out,
err_stream=f_err)
err_data = f_err.getvalue()
self.assertTrue("'--skipgml', "
"'--k', '5', "
"'--maxres', "
"'25.0', '--p', '75', "
"'--alg', 'leiden'" in err_data)
out_data = f_out.getvalue()
self.assertEqual(4087, len(out_data))
self.assertEqual(0, res)
finally:
shutil.rmtree(temp_dir)
def test_build_optional_arguments_with_n(self):
myargs = ['i2',
'--n', '1',
'--k', '3',
'--maxres', '0.6',
'--p', '8',
'--alg', 'leiden',
'--hidefcmd', 'foo',
'--tempdir', 'yo']
res = cdhidefcmd._parse_arguments('desc', myargs)
optargs = cdhidefcmd.build_optional_arguments(res)
self.assertEqual('--n', optargs[0])
self.assertEqual('1', optargs[1])
self.assertEqual('--k', optargs[2])
self.assertEqual('3', optargs[3])
self.assertEqual('--maxres', optargs[4])
self.assertEqual('0.6', optargs[5])
self.assertEqual('--p', optargs[6])
self.assertEqual('8', optargs[7])
self.assertEqual('--alg', optargs[8])
self.assertEqual('leiden', optargs[9])
def test_parse_args_all_defaults(self):
myargs = ['inputarg']
res = cdhidefcmd._parse_arguments('desc', myargs)
self.assertEqual('inputarg', res.input)
self.assertEqual(None, res.n)
self.assertEqual(5, res.k)
self.assertEqual(25.0, res.maxres)
self.assertEqual(75, res.p)
self.assertEqual('leiden', res.alg)
self.assertEqual('hidef_finder.py', res.hidefcmd)
self.assertEqual('/tmp', res.tempdir)
def test_run_hidef_no_file(self):
temp_dir = tempfile.mkdtemp()
try:
tfile = os.path.join(temp_dir, 'foo')
myargs = [tfile]
f_out = io.StringIO()
f_err = io.StringIO()
theargs = cdhidefcmd._parse_arguments('desc', myargs)
res = cdhidefcmd.run_hidef(theargs, out_stream=f_out,
err_stream=f_err)
self.assertEqual(3, res)
self.assertEqual(tfile + ' is not a file',
f_err.getvalue())
self.assertEqual('', f_out.getvalue())
finally:
shutil.rmtree(temp_dir)
def test_build_optional_arguments(self):
myargs = ['i2']
res = cdhidefcmd._parse_arguments('desc', myargs)
optargs = cdhidefcmd.build_optional_arguments(res)
self.assertEqual('--k', optargs[0])
self.assertEqual('5', optargs[1])
self.assertEqual('--maxres', optargs[2])
self.assertEqual('25.0', optargs[3])
self.assertEqual('--p', optargs[4])
self.assertEqual('75', optargs[5])
self.assertEqual('--alg', optargs[6])
self.assertEqual('leiden', optargs[7])
def test_parse_args_custom_params(self):
myargs = ['i2',
'--n', '1',
'--k', '3',
'--maxres', '0.6',
'--p', '8',
'--alg', 'leiden',
'--hidefcmd', 'foo',
'--tempdir', 'yo']
res = cdhidefcmd._parse_arguments('desc', myargs)
self.assertEqual('i2', res.input)
self.assertEqual(1, res.n)
self.assertEqual(3, res.k)
self.assertEqual(0.6, res.maxres)
self.assertEqual(8, res.p)
self.assertEqual('leiden', res.alg)
self.assertEqual('foo', res.hidefcmd)
self.assertEqual('yo', res.tempdir)
