def main():
option_parser, opts, args =\
parse_command_line_parameters(**script_info)
if (opts.suppress_unit_tests and opts.suppress_script_usage_tests):
option_parser.error("You're suppressing both test types. Nothing to run.")
test_dir = abspath(dirname(__file__))
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 PICRUSt's unit tests, and keep track of any files which
# fail unit tests.
if not opts.suppress_unit_tests:
unittest_names = []
if not opts.unittest_glob:
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))
else:
for fp in glob(opts.unittest_glob):
fn = split(fp)[1]
if fn.startswith('test_') and fn.endswith('.py'):
unittest_names.append(abspath(fp))
unittest_names.sort()
for unittest_name in unittest_names:
print "Testing %s:\n" % unittest_name
command = '%s %s -v' % (python_name, unittest_name)
stdout, stderr, return_value = system_call(command)
print stderr
if not unittest_good_pattern.search(stderr):
if application_not_found_pattern.search(stderr):
missing_application_tests.append(unittest_name)
else:
bad_tests.append(unittest_name)
if not opts.suppress_script_usage_tests:
try:
from qiime.test import run_script_usage_tests
except ImportError:
print "QIIME not installed so not running script tests."
opts.suppress_script_usage_tests=True
else:
test_data_dir = join(get_picrust_project_dir(),'picrust_test_data')
scripts_dir = join(get_picrust_project_dir(),'scripts')
if opts.script_usage_tests != None:
script_usage_tests = opts.script_usage_tests.split(',')
else:
script_usage_tests = None
# Run the script usage testing functionality
script_usage_result_summary, num_script_usage_example_failures = \
run_script_usage_tests(
qiime_test_data_dir=test_data_dir,
qiime_scripts_dir=scripts_dir,
working_dir='/tmp/',
verbose=True,
tests=script_usage_tests,
failure_log_fp=None,
force_overwrite=True)
print "==============\nResult summary\n=============="
if not opts.suppress_unit_tests:
print "\nUnit test result summary\n------------------------\n"
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 PICRUSt features "+\
"you plan to use, this may not be critical.\n%s"\
% '\n'.join(missing_application_tests)
if not (missing_application_tests or bad_tests):
print "\nAll unit tests passed.\n\n"
if not opts.suppress_script_usage_tests:
print "\nScript usage test result summary\n------------------------------------\n"
print script_usage_result_summary
print ""
# If script usage tests weren't suppressed,we can't have any failures.
script_usage_tests_success = (opts.suppress_script_usage_tests or
num_script_usage_example_failures == 0)
# If any of the unit tests or script usage tests fail, or if we have any
# missing application errors, use return code 1 (as python's unittest
# module does to indicate one or more failures).
return_code = 1
if (len(bad_tests) == 0 and len(missing_application_tests) == 0 and
script_usage_tests_success):
return_code = 0
return return_code
def main():
option_parser, opts, args =\
parse_command_line_parameters(**script_info)
if (opts.suppress_unit_tests and opts.suppress_script_usage_tests):
option_parser.error("You're suppressing both test types. Nothing to run.")
test_dir = abspath(dirname(__file__))
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 PICRUSt's unit tests, and keep track of any files which
# fail unit tests.
if not opts.suppress_unit_tests:
unittest_names = []
if not opts.unittest_glob:
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))
else:
for fp in glob(opts.unittest_glob):
fn = split(fp)[1]
if fn.startswith('test_') and fn.endswith('.py'):
unittest_names.append(abspath(fp))
unittest_names.sort()
for unittest_name in unittest_names:
print "Testing %s:\n" % unittest_name
command = '%s %s -v' % (python_name, unittest_name)
stdout, stderr, return_value = system_call(command)
print stderr
if not unittest_good_pattern.search(stderr):
if application_not_found_pattern.search(stderr):
missing_application_tests.append(unittest_name)
else:
bad_tests.append(unittest_name)
if not opts.suppress_script_usage_tests:
try:
from qiime.test import run_script_usage_tests
except ImportError:
print "QIIME not installed so not running script tests."
opts.suppress_script_usage_tests=True
else:
test_data_dir = join(get_picrust_project_dir(),'picrust_test_data')
scripts_dir = join(get_picrust_project_dir(),'scripts')
if opts.script_usage_tests != None:
script_usage_tests = opts.script_usage_tests.split(',')
else:
script_usage_tests = None
# Run the script usage testing functionality
script_usage_result_summary, num_script_usage_example_failures = \
run_script_usage_tests(
test_data_dir=test_data_dir,
scripts_dir=scripts_dir,
working_dir='/tmp/',
verbose=True,
tests=script_usage_tests,
force_overwrite=True,
timeout=300)
print "==============\nResult summary\n=============="
if not opts.suppress_unit_tests:
print "\nUnit test result summary\n------------------------\n"
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 PICRUSt features "+\
"you plan to use, this may not be critical.\n%s"\
% '\n'.join(missing_application_tests)
if not (missing_application_tests or bad_tests):
print "\nAll unit tests passed.\n\n"
if not opts.suppress_script_usage_tests:
print "\nScript usage test result summary\n------------------------------------\n"
print script_usage_result_summary
print ""
# If script usage tests weren't suppressed,we can't have any failures.
script_usage_tests_success = (opts.suppress_script_usage_tests or
num_script_usage_example_failures == 0)
# If any of the unit tests or script usage tests fail, or if we have any
# missing application errors, use return code 1 (as python's unittest
# module does to indicate one or more failures).
return_code = 1
if (len(bad_tests) == 0 and len(missing_application_tests) == 0 and
script_usage_tests_success):
return_code = 0
return return_code