def start_task(
self,
wid: str,
tool: Tool,
task_path: str,
environment: Environment,
hints: Dict[str, str],
validation_requirements: Optional[ValidationRequirements],
batchrun_requirements: Optional[BatchRunRequirements],
inputs_dict: dict = None,
dryrun=False,
watch=True,
max_cores=None,
max_memory=None,
keep_intermediate_files=False,
run_in_background=True,
dbconfig=None,
allow_empty_container=False,
container_override: dict = None,
check_files=True,
) -> WorkflowManager:
return WorkflowManager.from_janis(
wid,
tool=tool,
outdir=task_path,
environment=environment,
hints=hints,
inputs_dict=inputs_dict,
validation_requirements=validation_requirements,
batchrun_requirements=batchrun_requirements,
dryrun=dryrun,
watch=watch,
max_cores=max_cores,
max_memory=max_memory,
keep_intermediate_files=keep_intermediate_files,
run_in_background=run_in_background,
dbconfig=dbconfig,
allow_empty_container=allow_empty_container,
container_override=container_override,
check_files=check_files,
)
def run_from_jobfile(
workflow: Union[str, j.Tool, Type[j.Tool]],
jobfile: PreparedJob,
engine: Union[str, Engine, None] = None,
wait: bool = False,
# specific engine args
cromwell_jar: Optional[str] = None,
cromwell_url: Optional[str] = None,
):
cm = ConfigManager(db_path=jobfile.db_path)
if not workflow:
raise Exception("Couldn't find workflow with name: " + str(workflow))
row = cm.create_task_base(
wf=workflow,
job=jobfile,
)
jobfile.execution_dir = row.execution_dir
jobfile.output_dir = row.output_dir
# set logger for submit
Logger.set_write_level(Logger.CONSOLE_LEVEL)
logpath = os.path.join(
WorkflowManager.get_path_for_component_and_dir(
row.execution_dir, WorkflowManager.WorkflowManagerPath.logs),
"janis-submit.log",
)
Logger.WRITE_LEVELS = {Logger.CONSOLE_LEVEL: (logpath, open(logpath, "a"))}
Logger.debug(f"Set submission logging to '{logpath}'")
print(row.submission_id, file=sys.stdout)
eng = get_engine_from_eng(
engine or jobfile.engine,
wid=row.submission_id,
execdir=WorkflowManager.get_path_for_component_and_dir(
row.execution_dir, WorkflowManager.WorkflowManagerPath.execution),
confdir=WorkflowManager.get_path_for_component_and_dir(
row.execution_dir,
WorkflowManager.WorkflowManagerPath.configuration),
logfile=os.path.join(
WorkflowManager.get_path_for_component_and_dir(
row.execution_dir, WorkflowManager.WorkflowManagerPath.logs),
"engine.log",
),
cromwell_jar=cromwell_jar,
cromwell_url=cromwell_url,
)
try:
wm = WorkflowManager.from_janis(
submission_id=row.submission_id,
tool=workflow,
engine=eng,
prepared_submission=jobfile,
wait=wait,
)
Logger.log("Finished starting task")
return wm
except KeyboardInterrupt:
Logger.info("Exiting...")
try:
wm.abort()
except:
pass
except Exception as e:
# Have to make sure we stop the engine if something happens when creating the task that causes
# janis to exit early
eng.stop_engine()
raise e
return wm