import os
import asyncio
import subprocess
from pathlib import Path
from datetime import datetime, timedelta
from prefect import flow, get_run_logger, task
from prefect.cache_policies import NO_CACHE
from prefect.client.orchestration import get_client
from prefect.client.schemas.filters import (
FlowRunFilter,
FlowRunFilterStartTime,
FlowRunFilterState,
FlowRunFilterStateType,
)
from prefect.client.schemas.objects import StateType
from sqlalchemy.orm import aliased
from punchpipe.control.db import File, FileRelationship, Flow
from punchpipe.control.util import get_database_session, load_pipeline_configuration
[docs]
@flow
async def cleaner(pipeline_config_path: str, session=None):
logger = get_run_logger()
pipeline_config = load_pipeline_configuration(pipeline_config_path)
if session is None:
session = get_database_session()
reset_revivable_flows(logger, session, pipeline_config)
# because flows in the launched state aren't running in Prefect yet, we don't update them there
await fail_stuck_flows(logger, session, pipeline_config, "launched", update_prefect=False)
# running flows are both in Prefect and in our punchpipe database, so we have to cancel them both places
await fail_stuck_flows(logger, session, pipeline_config, "running", update_prefect=True)
[docs]
@task(cache_policy=NO_CACHE)
def reset_revivable_flows(logger, session, pipeline_config):
# Note: I thought about adding a maximum here, but this flow takes only 5 seconds to revive 10,000 L1 flows, so I
# think we're good.
child = aliased(File)
parent = aliased(File)
results = (session.query(FileRelationship, parent, child, Flow)
.join(parent, parent.file_id == FileRelationship.parent)
.join(child, child.file_id == FileRelationship.child)
.join(Flow, Flow.flow_id == child.processing_flow)
.where(Flow.state == 'revivable')
).all()
# This one loops differently than the others, because we need to track the child that's being deleted to know how
# to reset the parent.
unique_parents = set()
for _, parent, child, processing_flow in results:
# Handle the case that both L2 and LQ have been set to 'revivable'. If the LQ shows up first in this loop and
# we set the L1's state to 'created', we don't want to later set it to 'quickpunched' when the L2 shows up.
if processing_flow.flow_type not in ('construct_stray_light',
'construct_dynamic_stray_light'
'construct_f_corona_background',
'construct_starfield_background',
'levelq_CFM',):
parent.state = "created"
unique_parents.add(parent.file_id)
logger.info(f"Reset {len(unique_parents)} parent files")
unique_children = {child for rel, parent, child, flow in results}
root_path = Path(pipeline_config["root"])
for child in unique_children:
output_path = Path(child.directory(pipeline_config["root"])) / child.filename()
if output_path.exists():
os.remove(output_path)
sha_path = str(output_path) + '.sha'
if os.path.exists(sha_path):
os.remove(sha_path)
jp2_path = output_path.with_suffix('.jp2')
if jp2_path.exists():
os.remove(jp2_path)
# Iteratively remove parent directories if they're empty. output_path.parents gives the file's parent dir,
# then that dir's parent, then that dir's parent...
for parent_dir in output_path.parents:
if not parent_dir.exists():
break
if len(os.listdir(parent_dir)):
break
if parent_dir == root_path:
break
parent_dir.rmdir()
session.delete(child)
logger.info(f"Deleted {len(unique_children)} child files")
# Every FileRelationship item is unique
for relationship, _, _, _ in results:
session.delete(relationship)
logger.info(f"Cleared {len(results)} file relationships")
unique_flows = {flow for rel, parent, child, flow in results}
for f in unique_flows:
session.delete(f)
logger.info(f"Deleted {len(unique_flows)} flows")
session.commit()
if len(unique_flows):
logger.info(f"Processed {len(unique_flows)} revivable flows")
[docs]
@task(cache_policy=NO_CACHE)
async def cancel_running_prefect_flows_before_cutoff(
cutoff: datetime,
batch_size: int = 100
):
"""Cancels flows that started running before a cutoff time."""
logger = get_run_logger()
async with get_client() as client:
flow_run_filter = FlowRunFilter(
start_time=FlowRunFilterStartTime(before_=cutoff),
state=FlowRunFilterState(
type=FlowRunFilterStateType(
any_=[StateType.RUNNING]
)
)
)
# Get flow runs to delete
flow_runs = await client.read_flow_runs(
flow_run_filter=flow_run_filter,
limit=batch_size
)
if not flow_runs:
logger.info("No flows to delete")
return
n_cancelled = 0
while flow_runs:
# Cancel each flow run through the API
for i, flow_run in enumerate(flow_runs):
# First we send a cancel signal. If the underlying is process actually is still running, we don't
# want to leave it running unmonitored. (Ideally we wouldn't be cancelling it at all, but failing
# that, this is the next best thing.) There doesn't appear to be a way to cancel flows from the
# python client, so we have to roll up our sleeves. There also doesn't appear to be a way to get the
# PID of the underlying flow so we can kill it ourselves.
logger.info(f"Cancelling flow {flow_run.name}")
subprocess.run(["prefect", "flow-run", "cancel", str(flow_run.id)])
n_cancelled += 1
# Rate limiting - adjust based on your API capacity
if i % 10 == 0:
await asyncio.sleep(0.5)
logger.info(f"Cancelled a batch of {len(flow_runs)} flow runs (total: {n_cancelled})")
# Delay between batches to avoid overwhelming the API
await asyncio.sleep(1.0)
# Get next batch
flow_runs = await client.read_flow_runs(
flow_run_filter=flow_run_filter,
limit=batch_size
)
# Give time for Prefect to kill the processes
logger.info("Giving time for cancellations to happen...")
await asyncio.sleep(30)
# *Now* we can delete them. If they cancelled properly there's probably no need, but anecdotally if you try
# to cancel a flow when the underlying process isn't there (e.g. if you restarted the pipeline, and this
# flow is from before the restart), the cancellation never completes, and we need to make sure concurrency slots
# get freed. So we re-check for stuck running flows and delete those that failed to cancel.
flow_runs = await client.read_flow_runs(
flow_run_filter=flow_run_filter,
limit=batch_size
)
deleted_total = 0
failed_deletes = []
while flow_runs:
for i, flow_run in enumerate(flow_runs):
try:
logger.info(f"Deleting {flow_run.name} from Prefect")
await client.delete_flow_run(flow_run.id)
deleted_total += 1
except Exception as e:
logger.warning(f"Failed to delete flow run {flow_run.id}: {e}")
failed_deletes.append(flow_run.id)
# Rate limiting - adjust based on your API capacity
if i % 10 == 0:
await asyncio.sleep(0.5)
logger.info(f"Deleted a batch of {len(flow_runs)} flow runs (total: {deleted_total})")
# Delay between batches to avoid overwhelming the API
await asyncio.sleep(1.0)
# Get next batch
flow_runs = await client.read_flow_runs(
flow_run_filter=flow_run_filter,
limit=batch_size
)
logger.info(f"Deleted {deleted_total} flow runs")
if failed_deletes:
logger.warning(f"Failed to delete {len(failed_deletes)} flow runs")
[docs]
@task(cache_policy=NO_CACHE)
async def fail_stuck_flows(logger, session, pipeline_config, state, update_prefect=False):
amount_of_patience = pipeline_config['control']['cleaner'].get(f'fail_{state}_flows_after_minutes', -1)
if amount_of_patience < 0:
logger.warning(f"There is no fail_{state}_flows_after_minutes option in the config, so ending without checking.")
return
# First, we get the flows that are stuck. This should happen before the flows are killed, in case the flow's
# on_failure hook is able to change the flow state.
cutoff = datetime.now() - timedelta(minutes=amount_of_patience)
stucks = (session.query(Flow)
.where(Flow.state == state)
.where(Flow.launch_time < cutoff)
).all()
# Next we try to kill any of the stuck flows that are still running, so they release any DB locks they hold.
# we clean the prefect database even if our database returned no stucks because they might have somehow gotten
# out of sync. we want to clean that up too
if update_prefect:
# The postgres database has timezone-aware timestamps
local_timezone = datetime.now().astimezone().tzinfo
cutoff = cutoff.replace(tzinfo=local_timezone)
await cancel_running_prefect_flows_before_cutoff(cutoff)
# With the locks hopefully released, we can change the DB states
if len(stucks):
for stuck in stucks:
stuck.state = 'timed_out'
logger.info(f"Timing out flow {stuck.flow_id} {stuck.flow_run_name}")
# Mark the output files as timed_out
files = session.query(File).where(File.processing_flow.in_([s.flow_id for s in stucks])).all()
for file in files:
file.state = 'timed_out'
session.commit()
logger.info(f"Failed {len(stucks)} flows that have been "
f"in a '{state}' state for {amount_of_patience} minutes from punchpipe database")
