def test_validate_ISAtab_example(self):
from isatools.examples import validateISAtab
old_stdout = sys.stdout
sys.stdout = mystdout = StringIO()
args = ['validateISAtab.py', os.path.join(utils.TAB_DATA_DIR, 'BII-I-1', 'i_investigation.txt')]
validateISAtab.main(args)
sys.stdout = old_stdout
self.assertIn("Validated 1 ISA-Tab archives, 1 valid ISA-Tab archives, 0 invalid ISA-Tab archives", mystdout.getvalue())
self.assertIn("Found 0 errors and 40 warnings in across all ISA-Tab archives", mystdout.getvalue())
def test_validate_ISAtab_example_skip_file(self):
from isatools.examples import validateISAtab
old_stdout = sys.stdout
sys.stdout = mystdout = StringIO()
args = ['validateISAtab.py', os.path.join(utils.TAB_DATA_DIR, 'BII-I-1', 'i_investigation.tx')]
validateISAtab.main(args)
sys.stdout = old_stdout
self.assertIn("Validated 0 ISA-Tab archives, 0 valid ISA-Tab archives, 0 invalid ISA-Tab archives",
mystdout.getvalue())
def test_validate_ISAtab_example_invalid(self):
from isatools.examples import validateISAtab
with self.assertRaises(SystemExit):
old_stdout = sys.stdout
sys.stdout = mystdout = StringIO()
args = ['validateISAtab.py', os.path.join(utils.TAB_DATA_DIR, 'i_invalid', 'i_01.txt')]
validateISAtab.main(args)
sys.stdout = old_stdout
self.assertIn("Validated 1 ISA-Tab archives, 0 valid ISA-Tab archives, 1 invalid ISA-Tab archives",
mystdout.getvalue())
def test_validate_ISAtab_example_wrong_args(self):
from isatools.examples import validateISAtab
with self.assertRaises(SystemExit) as cm:
validateISAtab.main([])
self.assertEqual(cm.exception.code, 1)