def test_sample_sheet_path(self):
fc = BaseFlowcell.init_flowcell(self.original_flowcell)
sample_sheet = os.path.join(fc.path, 'SampleSheet.csv')
sample_sheet_renamed = os.path.join(fc.path, 'SamapleSheet.csv.bckp')
os.rename(sample_sheet, sample_sheet_renamed)
sample_sheet_path = os.path.join("tests/test_data/sample_sheets/hiseqx", fc.name, 'SampleSheet.csv')
sample_sheet_parser = SampleSheetParser(sample_sheet_path)
self.assertEqual(fc.sample_sheet, sample_sheet_parser.data)
os.rename(sample_sheet_renamed, sample_sheet)
def test_sample_sheet_path(self):
fc = BaseFlowcell.init_flowcell(self.original_flowcell)
sample_sheet = os.path.join(fc.path, 'SampleSheet.csv')
sample_sheet_renamed = os.path.join(fc.path, 'SamapleSheet.csv.bckp')
os.rename(sample_sheet, sample_sheet_renamed)
sample_sheet_path = os.path.join(
"tests/test_data/sample_sheets/hiseqx", fc.name, 'SampleSheet.csv')
sample_sheet_parser = SampleSheetParser(sample_sheet_path)
self.assertEqual(fc.sample_sheet, sample_sheet_parser.data)
os.rename(sample_sheet_renamed, sample_sheet)
def get_running_flowcells(self):
flowcells = []
for data_folder in self.config.get('data_folders', []):
# go through subfolders
subfolders = filter(os.path.isdir, [os.path.join(data_folder, fc_path) for fc_path in os.listdir(data_folder)])
for flowcell_path in subfolders:
# skip non-flowcell foldersd
if not re.match(FC_NAME_RE, os.path.basename(flowcell_path)):
logging.warning("Flowcell name doesn't match regex: {}".format(flowcell_path))
continue
# depending on the type, return instance of related class (hiseq, hiseqx, miseq, etc)
flowcell = BaseFlowcell.init_flowcell(path=flowcell_path)
flowcells.append(flowcell)
return flowcells
def get_nosync_flowcells(self):
flowcells = []
# check nosync folder
for data_folder in self.config.get('data_folders', []):
nosync_folder = os.path.join(data_folder, 'nosync')
if os.path.exists(nosync_folder):
# move flowcell to nosync list
for flowcell_name in os.listdir(nosync_folder):
flowcell_path = os.path.join(nosync_folder, flowcell_name)
# skip non-flowcell folders
if not re.match(FC_NAME_RE, os.path.basename(flowcell_path)):
logging.warning("Flowcell name doesn't match regex: {}".format(flowcell_path))
continue
flowcell = BaseFlowcell.init_flowcell(flowcell_path)
flowcells.append(flowcell)
return flowcells
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 test_seq_demux_started_done(self):
fc = BaseFlowcell(self.original_flowcell)
self.assertIsNotNone(fc.sequencing_started)
# self.assertEqual(type(fc.sequencing_started), type(datetime.datetime))
self.assertIsNotNone(fc.sequencing_done)
# self.assertEqual(type(fc.sequencing_done), type(datetime.datetime))
self.assertIsNotNone(fc.demultiplexing_started)
# self.assertEqual(type(fc.demultiplexing_started), type(datetime))
self.assertIsNotNone(fc.demultiplexing_done)
datetime_set = {
type(fc.sequencing_started),
type(fc.sequencing_done),
type(fc.demultiplexing_started),
type(fc.demultiplexing_done)
}
self.assertSetEqual({type(datetime.datetime.now())}, datetime_set)
def get_nosync_flowcells(self):
flowcells = []
# check nosync folder
for data_folder in self.config.get('data_folders', []):
nosync_folder = os.path.join(data_folder, 'nosync')
if os.path.exists(nosync_folder):
# move flowcell to nosync list
for flowcell_name in os.listdir(nosync_folder):
flowcell_path = os.path.join(nosync_folder, flowcell_name)
# skip non-flowcell folders
if not re.match(FC_NAME_RE,
os.path.basename(flowcell_path)):
logging.warning(
"Flowcell name doesn't match regex: {}".format(
flowcell_path))
continue
flowcell = BaseFlowcell.init_flowcell(flowcell_path)
flowcells.append(flowcell)
return flowcells
def get_running_flowcells(self):
flowcells = []
for data_folder in self.config.get('data_folders', []):
# go through subfolders
subfolders = filter(os.path.isdir, [
os.path.join(data_folder, fc_path)
for fc_path in os.listdir(data_folder)
])
for flowcell_path in subfolders:
# skip non-flowcell foldersd
if not re.match(FC_NAME_RE, os.path.basename(flowcell_path)):
logging.warning(
"Flowcell name doesn't match regex: {}".format(
flowcell_path))
continue
# depending on the type, return instance of related class (hiseq, hiseqx, miseq, etc)
flowcell = BaseFlowcell.init_flowcell(path=flowcell_path)
flowcells.append(flowcell)
return flowcells
def test_check_status(self):
fc = BaseFlowcell.init_flowcell(self.original_flowcell)
self.assertEqual(fc.status, FC_STATUSES['CHECKSTATUS'])
self.assertIsNotNone(fc.check_status)
def test_due_date(self):
fc = BaseFlowcell.init_flowcell(self.original_flowcell)
self.assertGreater(datetime.datetime.now(), fc.due_date)
def test_sequencing_started(self):
fc = BaseFlowcell.init_flowcell(self.original_flowcell)
self.assertIsNotNone(fc.sequencing_started)
def test_init_flowcell(self):
fc = BaseFlowcell.init_flowcell(self.original_flowcell)
self.assertIsInstance(fc, HiseqxFlowcell)
def test_run_info_present(self):
fc = BaseFlowcell(path=self.original_flowcell)
self.assertIsNotNone(fc.run_info)
self.assertIsNotNone(fc.run_parameters)
self.assertIsNotNone(fc.cycle_times)
self.assertIsNotNone(fc.sample_sheet)
def test_path(self):
fc = BaseFlowcell(self.original_flowcell)
self.assertEqual(self.original_flowcell, fc.path)
def test_init_flowcell(self):
fc = BaseFlowcell.init_flowcell(self.original_flowcell)
self.assertIsInstance(fc, HiseqFlowcell)
def test_sequencing_started(self):
fc = BaseFlowcell.init_flowcell(self.original_flowcell)
self.assertIsNotNone(fc.sequencing_started)
def test_due_date(self):
fc = BaseFlowcell.init_flowcell(self.original_flowcell)
self.assertGreater(datetime.datetime.now(), fc.due_date)
def test_check_status(self):
fc = BaseFlowcell.init_flowcell(self.original_flowcell)
self.assertEqual(fc.status, FC_STATUSES['CHECKSTATUS'])
self.assertIsNotNone(fc.check_status)
