def __init__(self, **kwargs):
verbosity = kwargs.pop('verbosity', 1)
if verbosity != 2:
logger.disable('DEBUG')
if kwargs.get('testRunner') is None:
kwargs['testRunner'] = TestRunner(verbosity=verbosity)
unittest.TestProgram.__init__(self, **kwargs)
def __init__(self, **kwargs):
verbosity = kwargs.pop('verbosity', 1)
if verbosity != 2:
logger.disable('DEBUG')
if kwargs.get('testRunner') is None:
kwargs['testRunner'] = TestRunner(verbosity=verbosity)
unittest.TestProgram.__init__(self, **kwargs)
def run(targets, options):
"Imports and runs the modules names that are contained in the 'targets'"
success = errors = skipped = 0
import_modules = [ 'doc_tests' ]
# run the tests by importing the module and getting its test suite
for name in targets:
try:
if name in import_modules:
mod = __import__(name)
suite = mod.get_suite()
else:
loader = unittest.TestLoader()
suite = loader.loadTestsFromName(name)
runner = TestRunner(verbosity=options.verbosity,
descriptions=0)
results = runner.run(suite)
# count tests and errors
success += results.testsRun - \
len(results.errors) - \
len(results.failures) - \
len(results.skipped)
errors += len(results.errors) + len(results.failures)
skipped += len(results.skipped)
# if we're in strict mode stop on errors
if options.strict and errors:
testutil.error( "strict mode stops on errors" )
break
except ImportError:
testutil.error( "unable to import module '%s'" % name )
# enable the logger
logger.disable(None)
# summarize the run
testutil.info('=' * 59)
testutil.info('''%s tests passed, %s tests failed, %s tests skipped; %d total''' % \
(success, errors, skipped, success + errors + skipped))
return (success, errors, skipped)
def run(targets, options):
"Imports and runs the modules names that are contained in the 'targets'"
success = errors = skipped = 0
import_modules = ['doc_tests']
# run the tests by importing the module and getting its test suite
for name in targets:
try:
if name in import_modules:
mod = __import__(name)
suite = mod.get_suite()
else:
loader = unittest.TestLoader()
suite = loader.loadTestsFromName(name)
runner = TestRunner(verbosity=options.verbosity, descriptions=0)
results = runner.run(suite)
# count tests and errors
success += results.testsRun - \
len(results.errors) - \
len(results.failures) - \
len(results.skipped)
errors += len(results.errors) + len(results.failures)
skipped += len(results.skipped)
# if we're in strict mode stop on errors
if options.strict and errors:
testutil.error("strict mode stops on errors")
break
except ImportError:
testutil.error("unable to import module '%s'" % name)
# enable the logger
logger.disable(None)
# summarize the run
testutil.info('=' * 59)
testutil.info('''%s tests passed, %s tests failed, %s tests skipped; %d total''' % \
(success, errors, skipped, success + errors + skipped))
return (success, errors, skipped)
'-x', '--index', action="store_true",
dest="index", default=False,
help="treat input file as binary index"
)
return parser
if __name__ == '__main__':
import optparse
parser = option_parser()
options, args = parser.parse_args()
logger.disable(options.verbosity)
from genetrack import conf
# trigger test mode
if options.test:
options.inpname = conf.testdata('test-hdflib-input.gtrack')
options.outname = conf.testdata('predictions.bed')
# missing input file name
if not options.inpname and not options.outname:
parser.print_help()
else:
print 'Sigma = %s' % options.sigma
print 'Minimum peak = %s' % options.level
print 'Peak-to-peak = %s' % options.exclude
import os, unittest, random
import testlib
from genetrack import conf, util, logger
class Hdflib( unittest.TestCase ):
'basic sequence class tests'
def test_all(self):
"Testing sequence operations"
#self.assertEqual(1, 0)
def get_suite():
"Returns the testsuite"
tests = [
Hdflib,
]
return testlib.make_suite( tests )
if __name__ == '__main__':
suite = get_suite()
logger.disable(None)
unittest.TextTestRunner(verbosity=2).run( suite )
from genetrack.scripts import tabs2genetrack
from genetrack import logger
if __name__ == "__main__":
import os
os.environ['LC_ALL'] = 'C'
#os.system( 'export' )
parser = tabs2genetrack.option_parser()
options, args = parser.parse_args()
# uppercase the format
options.format = options.format.upper()
if options.format not in ('BED', 'GFF'):
sys.stdout = sys.stderr
parser.print_help()
sys.exit(-1)
logger.disable(options.verbosity)
# missing file names
if not (options.inpname and options.outname and options.format):
parser.print_help()
sys.exit(-1)
else:
tabs2genetrack.transform(inpname=options.inpname, outname=options.outname,\
format=options.format, shift=options.shift, index=options.index, options=options)
data = authorize.create_data(user=john,
pid=project.id,
stream=stream,
name="Test data")
# project counts update
project = authorize.get_project(user=john, pid=project.id)
self.assertEqual(project.data_count, 1)
# testing data deletion
authorize.delete_data(user=john, pid=project.id, dids=[data.id])
project = authorize.get_project(user=john, pid=project.id)
self.assertEqual(project.data_count, 0)
def test_two(self):
pass
def get_suite():
"Returns the testsuite"
tests = [
AuthorizeTest,
]
return testlib.make_suite(tests)
if __name__ == '__main__':
suite = get_suite()
logger.disable('DEBUG')
unittest.TextTestRunner(verbosity=2).run(suite)
import os, unittest, random
import testlib
from genetrack import conf, util, logger
class Hdflib(unittest.TestCase):
'basic sequence class tests'
def test_all(self):
"Testing sequence operations"
#self.assertEqual(1, 0)
def get_suite():
"Returns the testsuite"
tests = [
Hdflib,
]
return testlib.make_suite(tests)
if __name__ == '__main__':
suite = get_suite()
logger.disable(None)
unittest.TextTestRunner(verbosity=2).run(suite)
# parse the options
options, args = parser.parse_args()
# modules: from command line args or all modules
targets = args or all_tests()
# get rid of the .py ending in case full module names were
# passed in the command line
targets = [t.rstrip(".py") for t in targets]
# exclusion mode
if options.exclude:
targets = [name for name in all_tests() if name not in targets]
if options.verbosity == 0:
logger.disable('INFO')
elif options.verbosity == 1:
logger.disable('DEBUG')
elif options.verbosity >= 2:
logger.disable(None)
# cleans full entire test directory
if options.reset:
conf.reset_dir(conf.TEMP_DATA_DIR)
# run all the tests
if options.coverage:
coverdir = conf.path_join(conf.TEST_DIR, 'coverage')
good, bad, skip = testutil.generate_coverage(run,
coverdir,
targets=targets,
from genetrack.server.web import authorize
john = User.objects.get(username='******')
project = authorize.create_project(user=john, name="Test project")
stream = File( open(conf.testdata('test-users.csv')) )
data = authorize.create_data(user=john, pid=project.id, stream=stream, name="Test data")
# project counts update
project = authorize.get_project(user=john, pid=project.id)
self.assertEqual(project.data_count, 1)
# testing data deletion
authorize.delete_data(user=john, pid=project.id, dids=[data.id])
project = authorize.get_project(user=john, pid=project.id)
self.assertEqual(project.data_count, 0)
def test_two(self):
pass
def get_suite():
"Returns the testsuite"
tests = [
AuthorizeTest,
]
return testlib.make_suite( tests )
if __name__ == '__main__':
suite = get_suite()
logger.disable('DEBUG')
unittest.TextTestRunner(verbosity=2).run( suite )
# parse the options
options, args = parser.parse_args()
# modules: from command line args or all modules
targets = args or all_tests()
# get rid of the .py ending in case full module names were
# passed in the command line
targets = [ t.rstrip(".py") for t in targets ]
# exclusion mode
if options.exclude:
targets = [ name for name in all_tests() if name not in targets ]
if options.verbosity == 0:
logger.disable('INFO')
elif options.verbosity == 1:
logger.disable('DEBUG')
elif options.verbosity >= 2:
logger.disable(None)
# cleans full entire test directory
if options.reset:
conf.reset_dir(conf.TEMP_DATA_DIR)
# run all the tests
if options.coverage:
coverdir = conf.path_join(conf.TEST_DIR, 'coverage')
good, bad, skip = testutil.generate_coverage(run, coverdir,
targets=targets,
options=options)
