def test_f(self):
cwd = os.getcwd()
recipe_test_dir = os.path.join(gs.TEST_DIR, 'recipe/task')
with execute_in_dir(recipe_test_dir):
self.assertEqual(os.path.join(cwd, recipe_test_dir), os.getcwd())
self.assertEqual(cwd, os.getcwd())
try:
with execute_in_dir(recipe_test_dir):
self.assertEqual(os.path.join(cwd, recipe_test_dir), os.getcwd())
assert(False)
except:
self.assertEqual(cwd, os.getcwd())
self.assertEqual(cwd, os.getcwd())
def run(self, task_id, resume_job=False, logging_thread=None):
"""
This function is executed to run this job.
:param int task_id:
:param bool resume_job:
:param sisyphus.worker.LoggingThread logging_thread:
"""
logging.debug("Task name: %s id: %s" % (self.name(), task_id))
job = self._job
logging.info("Start Job: %s Task: %s" % (job, self.name()))
logging.info("Inputs:")
for i in self._job._sis_inputs:
logging.info(str(i))
# each input must be at least X seconds old
# if an input file is too young it's may not synced in a network filesystem yet
try:
input_age = time.time() - os.stat(i.get_path()).st_mtime
time.sleep(max(0, gs.WAIT_PERIOD_MTIME_OF_INPUTS - input_age))
except FileNotFoundError:
logging.warning('Input path does not exist: %s' % i.get_path())
if i.creator and gs.ENABLE_LAST_USAGE:
# mark that input was used
try:
os.unlink(
os.path.join(i.creator, gs.JOB_LAST_USER,
os.getlogin()))
except OSError as e:
if e.errno not in (2, 13):
# 2: file not found
# 13: permission denied
raise e
try:
user_path = os.path.join(i.creator, gs.JOB_LAST_USER,
os.getlogin())
os.symlink(os.path.abspath(job._sis_path()), user_path)
os.chmod(user_path, 0o775)
except OSError as e:
if e.errno not in (2, 13, 17):
# 2: file not found
# 13: permission denied
# 17: file exists
raise e
tools.get_system_informations(sys.stdout)
sys.stdout.flush()
try:
if resume_job:
if self._resume is not None:
task = self._resume
else:
task = self._start
logging.warning(
'No resume function set (changed tasks after job was initialized?) '
'Fallback to normal start function: %s' % task)
else:
task = self._start
assert task is not None, "Error loading task"
# save current directory and change into work directory
with tools.execute_in_dir(self.path(gs.JOB_WORK_DIR)):
f = getattr(self._job, task)
# get job arguments
for arg_id in self._get_arg_idx_for_task_id(task_id):
args = self._args[arg_id]
if not isinstance(args, (list, tuple)):
args = [args]
logging.info("-" * 60)
logging.info("Starting subtask for arg id: %d args: %s" %
(arg_id, str(args)))
logging.info("-" * 60)
f(*args)
except sp.CalledProcessError as e:
if e.returncode == 137:
# TODO move this into engine class
logging.error(
"Command got killed by SGE (probably out of memory):")
logging.error("Cmd: %s" % e.cmd)
logging.error("Args: %s" % str(e.args))
logging.error("Return-Code: %s" % e.returncode)
logging_thread.out_of_memory = True
logging_thread.stop()
else:
logging.error("Executed command failed:")
logging.error("Cmd: %s" % e.cmd)
logging.error("Args: %s" % str(e.args))
logging.error("Return-Code: %s" % e.returncode)
logging_thread.stop()
self.error(task_id, True)
except Exception as e:
# Job failed
logging.error("Job failed, traceback:")
sys.excepthook(*sys.exc_info())
logging_thread.stop()
self.error(task_id, True)
# TODO handle failed job
else:
# Job finished normally
logging_thread.stop()
if not self.continuable:
self.finished(task_id, True)
sys.stdout.flush()
sys.stderr.flush()
logging.info("Job finished successful")
def test_run(self):
with execute_in_dir(TEST_DIR):
from recipe.task.test import Test
job = Test(text=Path("input_text.gz"))
job._sis_setup_directory()