def cleanup_missing_tasks(self):
from tabulate import tabulate
rows: [TaskRow] = self.get_lazy_db_connection().get_all_tasks()
failed = []
for row in rows:
if not os.path.exists(row.outputdir):
failed.append((row.submission_id, row.outputdir))
continue
try:
_ = WorkflowManager.from_path_with_submission_id(
row.outputdir, row.submission_id, readonly=True
)
except Exception as e:
failed.append((row.submission_id, row.outputdir))
if failed:
Logger.warn(f"Removing the following tasks:\n" + tabulate(failed))
if "y" in str(input(f"Remove {len(failed)} tasks (Y / n)? ")).lower():
self.get_lazy_db_connection().remove_by_ids([r[0] for r in failed])
Logger.info("Cleaned up tasks")
else:
Logger.info("Skipping cleaning of tasks")
def get_from_path_or_submission(
self, submission_id, readonly: bool, perform_path_check=True
):
if perform_path_check:
expanded_path = fully_qualify_filename(submission_id)
if os.path.exists(expanded_path):
return WorkflowManager.from_path_get_latest_manager(
expanded_path, readonly=readonly
)
potential_submission = self.get_lazy_db_connection().get_by_id(submission_id)
if potential_submission:
return WorkflowManager.from_path_with_submission_id(
potential_submission.execution_dir,
submission_id=submission_id,
readonly=readonly,
)
raise Exception(
f"Couldn't find task with id='{submission_id}', and no directory was found "
)
def remove_task(self, task: Union[str, TaskRow], keep_output: bool):
if isinstance(task, str):
wid = task
task = self.get_lazy_db_connection().get_by_wid(task)
if task is None:
raise Exception("Couldn't find workflow with ID = " + wid)
tm = WorkflowManager.from_path_with_submission_id(
task.outputdir, task.submission_id
)
tm.cleanup_execution()
tm.database.close()
if not keep_output and os.path.exists(task.outputdir):
Logger.info("Removing " + task.outputdir)
rmtree(task.outputdir)
else:
Logger.info("Skipping output dir deletion, can't find: " + task.outputdir)
self.get_lazy_db_connection().remove_by_id(task.submission_id)
Logger.info("Deleted task: " + task.submission_id)