add an option to raise within tasks

Author: oliche

ibllib/pipes/tasks.py

@@ -112,9 +112,10 @@ class Task(abc.ABC):
     force = False  # whether to re-download missing input files on local server if not present
     job_size = 'small'  # either 'small' or 'large', defines whether task should be run as part of the large or small job services
     env = None  # the environment name within which to run the task (NB: the env is not activated automatically!)
+    on_error = 'continue'  # whether to raise an exception on error ('raise') or report the error and continue ('continue')
 
     def __init__(self, session_path, parents=None, taskid=None, one=None,
-                 machine=None, clobber=True, location='server', scratch_folder=None, **kwargs):
+                 machine=None, clobber=True, location='server', scratch_folder=None, on_error='continue', **kwargs):
         """
         Base task class
         :param session_path: session path
@@ -129,6 +130,18 @@ def __init__(self, session_path, parents=None, taskid=None, one=None,
         :param scratch_folder: optional: Path where to write intermediate temporary data
         :param args: running arguments
         """
+        self.on_error = on_error
+        self.log = ''  # placeholder to keep the log of the task for registration
+        self.cpu = kwargs.get('cpu', 1)
+        self.gpu = kwargs.get('gpu', 0)
+        self.io_charge = kwargs.get('io_charge', 5)
+        self.priority = kwargs.get('priority', 30)
+        self.ram = kwargs.get('ram', 4)
+        self.level = 0  # level in the pipeline hierarchy: level 0 means there is no parent task
+        self.outputs = []  # placeholder for a list of Path containing output files
+        self.time_elapsed_secs = None
+        self.time_out_secs = 3600 * 2  # time-out after which a task is considered dead
+        self.version = ibllib.__version__
         self.taskid = taskid
         self.one = one
         self.session_path = session_path
@@ -263,10 +276,12 @@ def run(self, **kwargs):
                 self.outputs = outputs if not self.outputs else self.outputs  # ensure None if no inputs registered
             else:
                 self.outputs.extend(ensure_list(outputs))  # Add output files to list of inputs to register
-        except Exception:
+        except Exception as e:
             _logger.error(traceback.format_exc())
             _logger.info(f'Job {self.__class__} errored')
             self.status = -1
+            if self.on_error == 'raise':
+                raise e
 
         self.time_elapsed_secs = time.time() - start_time
         # log the outputs