def sample_sheet(self):
if self._sample_sheet is None:
sample_sheet_path = os.path.join(self.path, 'SampleSheet.csv')
if os.path.exists(sample_sheet_path):
self._sample_sheet = SampleSheetParser(sample_sheet_path).data
else:
logging.warning("SampleSheet.csv does not exist: {}".format(
os.path.abspath(sample_sheet_path)))
path = config.get('sample_sheet_path', {}).get('hiseqx')
if path is None:
logging.error(
"'sample_sheet_path' missing in the config file")
raise RuntimeError(
"'sample_sheet_path' missing in the config file: {}".
format(config.get('config_path')))
else:
sample_sheet_path = os.path.join(path, self.name,
'SampleSheet.csv')
if os.path.exists(sample_sheet_path):
self._sample_sheet = SampleSheetParser(
sample_sheet_path).data
else:
logging.error(
"SampleSheet.csv does not exist at {}".format(
sample_sheet_path))
raise RuntimeError(
"SampleSheet.csv does not exist at {}".format(
sample_sheet_path))
return self._sample_sheet
def test_flowcells(hiseqx, hiseq, miseq, all):
""" Run unittests with the default config file: tests/config.yaml. To change it, edit tests/test_<fc-type>.py file"""
# load_yaml_config(config_file)
if not config.get('trello', ''):
logging.error("Config file missing required entries: 'trello'")
raise RuntimeError("Config file missing required entries: 'trello'")
if not config.get('data_folders', ''):
logging.error("Config file missing required entries: 'data_folders'")
raise RuntimeError(
"Config file missing required entries: 'data_folders'")
data_folders = []
for data_folder in config.get('data_folders'):
if not data_folder.startswith('/'):
script_path = os.path.realpath(__file__)
dirname = os.path.dirname(script_path)
abs_path = os.path.join(dirname, data_folder)
data_folders.append(abs_path)
config.update({'data_folders': data_folders})
if all or not any([hiseqx, hiseq, miseq]): # if no flags or flag=all
for Test in [TestMiseq, TestHiseq, TestHiseqX]:
suite = unittest.TestLoader().loadTestsFromTestCase(Test)
unittest.TextTestRunner(verbosity=2).run(suite)
else:
if hiseqx:
suite = unittest.TestLoader().loadTestsFromTestCase(TestHiseqX)
unittest.TextTestRunner(verbosity=2).run(suite)
if hiseq:
suite = unittest.TestLoader().loadTestsFromTestCase(TestHiseq)
unittest.TextTestRunner(verbosity=2).run(suite)
if miseq:
suite = unittest.TestLoader().loadTestsFromTestCase(TestMiseq)
unittest.TextTestRunner(verbosity=2).run(suite)
def monitor_flowcells():
""" Collect information from the filesystem and update the trello board"""
if not CONFIG.get('trello', ''):
logging.error("Config file missing required entries: 'trello'")
raise RuntimeError("Config file missing required entries: 'trello'")
if not CONFIG.get('data_folders', ''):
logging.error("Config file missing required entries: 'data_folders'")
raise RuntimeError(
"Config file missing required entries: 'data_folders'")
flowcell_monitor = FlowcellMonitor(CONFIG)
flowcell_monitor.update_trello_board()
def test_transferring(self):
fc = BaseFlowcell.init_flowcell(self.original_flowcell)
self.assertIsNotNone(fc.transfering_started)
# to make sure it's a datetime and nothing else
transfering = {
'hiseqx': {
'url': 'localhost',
'username': '******',
'path': os.path.join(os.path.abspath('tests/test_data/hiseqx')) #)'/Users/ekaterinastepanova/work/hugin/tests/test_data/hiseqx'
}
}
config.update({'transfering': transfering})
self.assertGreater(datetime.datetime.now(), fc.transfering_started)
def test_transferring(self):
fc = BaseFlowcell.init_flowcell(self.original_flowcell)
self.assertIsNotNone(fc.transfering_started)
# to make sure it's a datetime and nothing else
transfering = {
'hiseqx': {
'url': 'localhost',
'username': '******',
'path': os.path.join(
os.path.abspath('tests/test_data/hiseqx')
) #)'/Users/ekaterinastepanova/work/hugin/tests/test_data/hiseqx'
}
}
config.update({'transfering': transfering})
self.assertGreater(datetime.datetime.now(), fc.transfering_started)
def sample_sheet(self):
if self._sample_sheet is None:
sample_sheet_path = os.path.join(self.path, 'SampleSheet.csv')
if os.path.exists(sample_sheet_path):
self._sample_sheet = SampleSheetParser(sample_sheet_path).data
else:
logging.warning("SampleSheet.csv does not exist: {}".format(os.path.abspath(sample_sheet_path)))
path = config.get('sample_sheet_path', {}).get('hiseqx')
if path is None:
logging.error("'sample_sheet_path' missing in the config file")
raise RuntimeError("'sample_sheet_path' missing in the config file: {}".format(config.get('config_path')))
else:
sample_sheet_path = os.path.join(path, self.name, 'SampleSheet.csv')
if os.path.exists(sample_sheet_path):
self._sample_sheet = SampleSheetParser(sample_sheet_path).data
else:
logging.error("SampleSheet.csv does not exist at {}".format(sample_sheet_path))
raise RuntimeError("SampleSheet.csv does not exist at {}".format(sample_sheet_path))
return self._sample_sheet
def test_flowcell_monitor(self):
monitor = FlowcellMonitor(self.config)
data_folders = monitor.data_folders
self.assertEqual(data_folders, config.get('data_folders'))
def test_flowcell_monitor(self):
monitor = FlowcellMonitor(self.config)
data_folders = monitor.data_folders
self.assertEqual(data_folders, config.get('data_folders'))
