def test_sets_status_to_empty_when_recon_done_present(self, mock_exists):
recon_done = self.fs_path + '/scripts/recon-all.done'
mock_exists.side_effect = lambda x: True if x == recon_done else False
my_log = scraper.FSLog(self.fs_path)
assert my_log.status == ''
def test_sets_status_error_when_recon_error_present(self, mock_exists):
error_log = self.fs_path + '/scripts/recon-all.error'
mock_exists.side_effect = lambda x: True if x == error_log else False
my_log = scraper.FSLog(self.fs_path)
assert my_log.status == scraper.FSLog._ERROR
def test_sets_status_maybe_halted_when_IsRunning_log_unreadable(
self, mock_glob):
# Return path to nonexistent file
mock_glob.return_value = ["/some/path/IsRunning.lh+rh"]
my_log = scraper.FSLog(self.fs_path)
assert my_log.status == scraper.FSLog._MAYBE_HALTED
def test_sets_running_status_when_subject_running_less_than_24h(
self, mock_glob, mock_read_log):
mock_glob.return_value = ['/some/path/IsRunning.lh+rh']
# Time zone isnt taken into account when time is compared, but required
# by the date parsing code
now = datetime.datetime.now(tz=EST()).strftime(self.FS_date_format)
mock_read_log.return_value = ['DATE {}'.format(now)]
my_log = scraper.FSLog(self.fs_path)
assert my_log.status == scraper.FSLog._RUNNING
def get_site_standards(freesurfer_dir, args, subject_folder):
logger.debug("Using subject {} to generate standards.".format(subject_folder))
if not args:
return None
standard_log = fs_scraper.FSLog(subject_folder)
standards = {'build': standard_log.build,
'kernel': standard_log.kernel,
'args': args}
return standards
def test_sets_status_timedout_when_subject_running_more_than_24h(
self, mock_glob, mock_read_log):
mock_glob.return_value = ['/some/path/IsRunning.lh+rh']
two_days_ago = datetime.datetime.now(tz=EST()) - datetime.timedelta(2)
mock_read_log.return_value = [
'DATE {}'.format(two_days_ago.strftime(self.FS_date_format))
]
my_log = scraper.FSLog(self.fs_path)
assert my_log.status == scraper.FSLog._TIMEDOUT.format(
'IsRunning.lh+rh')
def get_halted_subjects(fs_path, subjects):
timed_out_msg = fs_scraper.FSLog._TIMEDOUT.format("")
halted = []
for subject in subjects:
if sid.is_phantom(subject):
continue
fs_folder = os.path.join(fs_path, subject)
try:
log = fs_scraper.FSLog(fs_folder)
except:
pass
else:
if log.status.startswith(timed_out_msg):
halted.append(subject)
return halted
def test_values_set_to_empty_when_recon_done_unreadable(
self, mock_exists, mock_read_log):
recon_done = self.fs_path + '/scripts/recon-all.done'
mock_exists.side_effect = lambda x: True if x == recon_done else False
mock_read_log.return_value = {}
my_log = scraper.FSLog(self.fs_path)
assert my_log.status == ''
# Subject will be set to basename of the freesurfer path if
# recon-all.done isnt present/is unreadable
# assert my_log.subject == ''
assert my_log.start == ''
assert my_log.end == ''
assert my_log.kernel == ''
assert my_log.args == ''
assert my_log.nii_inputs == ''