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# Copyright 2013 by Peter Cock. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""Bio.Application related tests for command line application wrappers.
This is intended to check generic things like argument parsing, and
stdin/stdout/stderr handling.
"""
import os
import unittest
import warnings
from Bio import BiopythonDeprecationWarning
with warnings.catch_warnings():
warnings.simplefilter("ignore", category=BiopythonDeprecationWarning)
from Bio.Application import _Argument
from Bio.Application import AbstractCommandline
class EchoApp(AbstractCommandline):
"""Minimal command line wrapper for echo command."""
def __init__(self, cmd="echo", **kwargs):
"""Initialize wrapper for echo command."""
self.parameters = [_Argument(["text"], "Text to echo")]
AbstractCommandline.__init__(self, cmd, **kwargs)
class TestApp(unittest.TestCase):
def test_echo(self):
cline = EchoApp(text="Hello World")
stdout, stderr = cline()
self.assertEqual(stderr, "")
self.assertEqual(stdout, "Hello World\n")
def test_echo_capture_both(self):
cline = EchoApp(text="Hello World")
stdout, stderr = cline(stdout=True, stderr=True)
self.assertEqual(stderr, "")
self.assertEqual(stdout, "Hello World\n")
def test_echo_capture_stdout(self):
cline = EchoApp(text="Hello World")
stdout, stderr = cline(stdout=True, stderr=False)
self.assertIsNone(stderr)
self.assertEqual(stdout, "Hello World\n")
def test_echo_capture_stderr(self):
cline = EchoApp(text="Hello World")
stdout, stderr = cline(stdout=False, stderr=True)
self.assertEqual(stderr, "")
self.assertIsNone(stdout)
def test_echo_capture_neither(self):
cline = EchoApp(text="Hello World")
stdout, stderr = cline(stdout=False, stderr=False)
self.assertIsNone(stderr)
self.assertIsNone(stdout)
def test_echo_file_stdout(self):
cline = EchoApp(text="Hello World")
tmp = "echo_stdout.tmp"
if os.path.isfile(tmp):
os.remove(tmp)
stdout, stderr = cline(stdout=tmp)
self.assertEqual(stderr, "")
self.assertIsNone(stdout)
self.assertTrue(os.path.isfile(tmp))
with open(tmp) as handle:
contents = handle.read()
self.assertEqual(contents, "Hello World\n")
os.remove(tmp)
def test_echo_file_stderr(self):
cline = EchoApp(text="Hello World")
tmp = "echo_stderr.tmp"
if os.path.isfile(tmp):
os.remove(tmp)
stdout, stderr = cline(stderr=tmp)
self.assertIsNone(stderr)
self.assertEqual(stdout, "Hello World\n")
self.assertTrue(os.path.isfile(tmp))
with open(tmp) as handle:
contents = handle.read()
self.assertEqual(contents, "")
os.remove(tmp)
def test_echo_file_same(self):
cline = EchoApp(text="Hello World")
tmp = "echo_stdout_stderr.tmp"
if os.path.isfile(tmp):
os.remove(tmp)
stdout, stderr = cline(stdout=tmp, stderr=tmp)
self.assertIsNone(stderr)
self.assertIsNone(stdout)
self.assertTrue(os.path.isfile(tmp))
with open(tmp) as handle:
contents = handle.read()
self.assertEqual(contents, "Hello World\n") # stdout + stderr
os.remove(tmp)
def test_echo_file_both(self):
cline = EchoApp(text="Hello World")
tmp = "echo_stdout.tmp"
if os.path.isfile(tmp):
os.remove(tmp)
tmp2 = "echo_stderr.tmp"
if os.path.isfile(tmp2):
os.remove(tmp2)
stdout, stderr = cline(stdout=tmp, stderr=tmp2)
self.assertIsNone(stderr)
self.assertIsNone(stdout)
self.assertTrue(os.path.isfile(tmp), tmp)
with open(tmp) as handle:
contents = handle.read()
self.assertEqual(contents, "Hello World\n") # stdout
os.remove(tmp)
self.assertTrue(os.path.isfile(tmp2), tmp2)
with open(tmp2) as handle:
contents = handle.read()
self.assertEqual(contents, "") # stderr
os.remove(tmp2)
if __name__ == "__main__":
runner = unittest.TextTestRunner(verbosity=2)
unittest.main(testRunner=runner)
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