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#!/usr/bin/env python
#-----------------------------------------------------------------------------
# Copyright (c) 2013, The PyNAST Development Team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
#-----------------------------------------------------------------------------
from os import walk, environ
from subprocess import Popen, PIPE, STDOUT
from os.path import join, abspath, dirname, split
from glob import glob
import re
def main():
pynast_dir = abspath(join(dirname(__file__),'..'))
test_dir = join(pynast_dir,'tests')
scripts_dir = join(pynast_dir,'scripts')
unittest_good_pattern = re.compile('OK\s*$')
application_not_found_pattern = re.compile('ApplicationNotFoundError')
python_name = 'python'
bad_tests = []
missing_application_tests = []
# Run through all of PyNAST's unit tests, and keep track of any files which
# fail unit tests.
unittest_names = []
for root, dirs, files in walk(test_dir):
for name in files:
if name.startswith('test_') and name.endswith('.py'):
unittest_names.append(join(root,name))
unittest_names.sort()
for unittest_name in unittest_names:
print "Testing %s:\n" % unittest_name
command = '%s %s -v' % (python_name, unittest_name)
result = Popen(command,shell=True,universal_newlines=True,\
stdout=PIPE,stderr=STDOUT).stdout.read()
print result
if not unittest_good_pattern.search(result):
if application_not_found_pattern.search(result):
missing_application_tests.append(unittest_name)
else:
bad_tests.append(unittest_name)
# Run through all of PyNAST's scripts, and pass -h to each one. If the
# resulting stdout does not being with the Usage text, that is an
# indicator of something being wrong with the script. Issues that would
# cause that are bad import statements in the script, SyntaxErrors, or
# other failures prior to running parse_command_line_parameters.
script_names = []
script_names = glob('%s/*' % scripts_dir)
script_names.sort()
bad_scripts = []
for script_name in script_names:
script_good_pattern = re.compile('^Usage: %s' % split(script_name)[1])
print "Testing %s." % script_name
command = '%s %s -h' % (python_name, script_name)
result = Popen(command,shell=True,universal_newlines=True,\
stdout=PIPE,stderr=STDOUT).stdout.read()
# remove warning cause by missing python-mpi4py
result = re.sub(r'(?m)^/usr/lib.*Not using MPI as mpi4py not found\n?', '', result)
result = re.sub(r'(?m)^\s*from cogent.util.parallel import MPI\n?', '', result)
if not script_good_pattern.search(result):
bad_scripts.append(script_name)
if bad_tests:
print "\nFailed the following unit tests.\n%s" % '\n'.join(bad_tests)
if missing_application_tests:
print "\nFailed the following unit tests, in part or whole due "+\
"to missing external applications.\nDepending on the QIIME features "+\
"you plan to use, this may not be critical.\n%s"\
% '\n'.join(missing_application_tests)
if bad_scripts:
print "\nFailed the following script tests.\n%s" % '\n'.join(bad_scripts)
# If any of the unit tests or script tests failed, or if we have any
# missing application errors, use return code 1 (as python's
# unittest module does) to indicate one or more failures with the test
# suite.
return_code = 1
if not (bad_tests or missing_application_tests or bad_scripts):
print "\nAll tests passed successfully."
return_code = 0
return return_code
if __name__ == "__main__":
exit(main())
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