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.wid, row.outputdir))
continue
try:
_ = WorkflowManager.from_path_with_wid(
row.outputdir, row.wid, readonly=True
)
except Exception as e:
failed.append((row.wid, 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 from_wid(self, wid, readonly=False):
self.readonly = readonly
with self.with_cursor() as cursor:
path = cursor.execute(
"SELECT outputdir FROM tasks where wid=?", (wid,)
).fetchone()
if not path:
expanded_path = fully_qualify_filename(wid)
if os.path.exists(expanded_path):
return WorkflowManager.from_path_get_latest(
expanded_path, readonly=readonly
)
raise Exception(f"Couldn't find task with id='{wid}'")
return WorkflowManager.from_path_with_wid(path[0], wid=wid, readonly=readonly)
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_wid(task.outputdir, task.wid)
tm.remove_exec_dir()
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.wid)
Logger.info("Deleted task: " + task.wid)