# coding: utf-8
from __future__ import print_function, division, absolute_import

import sys, os
from contextlib import contextmanager
from cutadapt.scripts import cutadapt

@contextmanager
def redirect_stderr():
	"Send stderr to stdout. Nose doesn't capture stderr, yet."
	old_stderr = sys.stderr
	sys.stderr = sys.stdout
	yield
	sys.stderr = old_stderr


@contextmanager
def temporary_path(name):
	directory = os.path.join(os.path.dirname(__file__), 'testtmp')
	if not os.path.isdir(directory):
		os.mkdir(directory)
	path = os.path.join(directory, name)
	yield path
	os.remove(path)


def datapath(path):
	return os.path.join(os.path.dirname(__file__), 'data', path)


def cutpath(path):
	return os.path.join(os.path.dirname(__file__), 'cut', path)


def files_equal(path1, path2):
	return os.system("diff -u {0} {1}".format(path1, path2)) == 0


def run(params, expected, inpath, inpath2=None):
	if type(params) is str:
		params = params.split()
	with temporary_path(expected) as tmp_fastaq:
		params += ['-o', tmp_fastaq ] # TODO not parallelizable
		params += [ datapath(inpath) ]
		if inpath2:
			params += [ datapath(inpath2) ]
		assert cutadapt.main(params) is None
		# TODO redirect standard output
		assert files_equal(cutpath(expected), tmp_fastaq)
	# TODO diff log files