def test_get_status_list(self):
"""Get the status list to write card to"""
run_folder = "120106_SN12345_0144_AABC123CXX"
run_path = os.path.join(self.dump_folder,run_folder)
os.mkdir(run_path)
flags = ['initial_processing_started.txt', 'initial_processing_completed.txt', 'first_read_processing_started.txt']
for f in flags:
with open(os.path.join(run_path,f),"w") as fh:
fh.write("{}Z".format(str(datetime.datetime.utcfromtimestamp(time.time() - 9*60*60))))
run = {'name': run_folder,
'path': run_path}
rm = RunMonitor(self.config)
rm.get_run_info = mock.Mock(return_value={'Reads': [{},{'IsIndexedRead': 'Y'},{'IsIndexedRead': 'Y'},{}]})
self.assertEqual(rm.get_status_list(run),
"Check status",
"Expected status list 'Check status'")
os.unlink(os.path.join(run_path,flags[-1]))
self.assertEqual(rm.get_status_list(run),
"First read",
"Expected status list 'First read'")
open(os.path.join(run_path,'Basecalling_Netcopy_complete_Read1.txt'),'w').close()
self.assertEqual(rm.get_status_list(run),
"Index read",
"Expected status list 'Index read'")
open(os.path.join(run_path,'Basecalling_Netcopy_complete_Read2.txt'),'w').close()
self.assertEqual(rm.get_status_list(run),
"Index read",
"Expected status list 'Index read'")
open(os.path.join(run_path,'Basecalling_Netcopy_complete_Read3.txt'),'w').close()
self.assertEqual(rm.get_status_list(run),
"Second read",
"Expected status list 'Second read'")
open(os.path.join(run_path,'Basecalling_Netcopy_complete_Read4.txt'),'w').close()
self.assertEqual(rm.get_status_list(run),
"Processing",
"Expected status list 'Processing'")
shutil.rmtree(run_path)
def test_list_runs(self):
"""List run folders"""
run_folders = ["120106_SN12345_0144_AABC123CXX",
"120521_M00123_0001_AFCGHY76-KTY500",
"130423_D00134_0011_AD1Y4UACXX"]
invalid_run_folders = ["ABC_SN123_0123_BASDC34CXX",
"120106_SN12345_0144_CABC123CXX",
"120521_K00123_0001_AFCGHY76-KTY500"]
for d in run_folders + invalid_run_folders:
os.mkdir(os.path.join(self.dump_folder,d))
rm = RunMonitor(self.config)
rm.get_run_info = mock.Mock(return_value={})
rm.get_run_parameters = mock.Mock(return_value={})
runs = rm.list_runs()
self.assertListEqual(sorted(run_folders),
sorted([r['name'] for r in runs]),
"Did not return expected list of runs")
for d in run_folders + invalid_run_folders:
shutil.rmtree(os.path.join(self.dump_folder,d))
def test_update_trello_board(self):
"""Update Trello list with runs"""
run_folders = ["120106_SN12345_0144_AABC123CXX",
"120521_M00123_0001_AFCGHY76-KTY500"]
for d in run_folders:
os.mkdir(os.path.join(self.dump_folder,d))
rm = RunMonitor(self.config)
rm.get_run_projects = mock.Mock(return_value=['J.Doe_11_01','J.Moe_12_02'])
rm.get_status_list = mock.Mock(return_value='First read')
rm.get_run_info = mock.Mock(return_value={'Reads': [{'NumCycles': 50},{'IsIndexedRead': 'Y'},{'NumCycles': 50}]})
rm.get_run_parameters = mock.Mock(return_value={})
rm.update_trello_board()
lst = rm.trello.get_list(rm.trello_board,'First read')
for run in run_folders:
card = rm.trello.get_card(lst,run)
self.assertIsNotNone(card,
"Could not locate created card for run")
self.assertEqual(run,
card.name,
"Created card name and run name are not equal")
shutil.rmtree(os.path.join(self.dump_folder,run))
# Move a card to another list
run = {'name': run_folders[0]}
rm.list_runs = mock.Mock(return_value=[run])
rm.get_status_list.return_value = 'Index read'
rm.update_trello_board()
lst = rm.trello.get_list(rm.trello_board,'Index read')
card = rm.trello.get_card(lst,run['name'])
self.assertIsNotNone(card,
"Could not locate created card for run")
self.assertEqual(run['name'],
card.name,
"Created card name and run name are not equal")