def test_send_notification(self):
"""Send an email notification"""
rm = RunMonitor(self.config)
exception = None
try:
rm.send_notification({'name': "test run"},"dummy value")
except Exception, e:
exception = e
def test_parse_description(self):
"""Parse a description"""
org_description = \
"""- extra comment
- project:J.Doe_11_02,J.Doe_12_01,J.Doe_13_01
- setup:2x101bp""".strip()
rm = RunMonitor(self.config)
org_metadata = rm.parse_description(org_description)
exp_description = rm.create_description(org_metadata)
exp_metadata = rm.parse_description(exp_description)
self.assertEqual(org_description,
exp_description,
"The recreated card description does not match the original")
self.assertDictEqual(org_metadata,
exp_metadata,
"The recreated card metadata does not match the original")
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_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_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")
def update_run_status(self):
"""Update the status of runs on the run tracking board"""
# Create a RunMonitor object to update the run tracking board
from hugin.run_monitor import RunMonitor
rm = RunMonitor(self.config)
rm.run_folders = self.archive_folders
rm.samplesheet_folders = []
# Loop over the runs and check whether all samples and projects have been transferred to the
# analysis folder
for run in rm.list_runs():
print("Checking run {}".format(run['name']))
if self.get_run_status(run):
rm.set_run_completed(run)
# Loop over the projects in the run and move them to the bcbb list
# Note that this can cause the card to be moved back to sequencing by the run_monitor in case
# the project is sequenced on multiple flowcells. Has no good solution at this moment.
for project in run.get('projects',[]):
self.add_project_card(project,BCBB_ANALYSIS_IN_PROGRESS)
def monitor(config,check_descrip,check_finish): rm = RunMonitor(config) if check_descrip: rm.check_missing_description() elif check_finish: rm.check_finish_status() else: rm.update_trello_board() rm.update_trello_project_board() rm.archive_cards()
def monitor(config):
rm = RunMonitor(config)
rm.update_trello_board()
rm.update_trello_project_board()
rm.archive_cards()
