Galaxy unable to delete jobs submitted through TES Pulsar library

[micoleaoo]

You can delete datasets throught UI but they still linger in database, resulting in nonstop cycle of these logs -->

Galaxy log:

Apr 11 07:57:24 galaxy-qa-nd-2 galaxyctl[875355]: galaxy.jobs.handler DEBUG 2025-04-11 07:57:24,426 [pN:handler_0,p:875355,tN:JobHandlerStopQueue.monitor_thread] Stopping job 260 in pulsar_tes runner
Apr 11 07:57:24 galaxy-qa-nd-2 galaxyctl[875355]: galaxy.jobs.runners.pulsar DEBUG 2025-04-11 07:57:24,438 [pN:handler_0,p:875355,tN:JobHandlerStopQueue.monitor_thread] Attempt remote Pulsar kill of job with url pulsar_tes and id 67f52f266dd4e6cf81e81e87
Apr 11 07:57:24 galaxy-qa-nd-2 galaxyctl[875355]: galaxy.jobs.handler ERROR 2025-04-11 07:57:24,467 [pN:handler_0,p:875355,tN:JobHandlerStopQueue.monitor_thread] Exception in monitor_step
Apr 11 07:57:24 galaxy-qa-nd-2 galaxyctl[875355]: Traceback (most recent call last):
Apr 11 07:57:24 galaxy-qa-nd-2 galaxyctl[875355]:   File "/srv/galaxy/venv/lib/python3.11/site-packages/requests/models.py", line 974, in json
Apr 11 07:57:24 galaxy-qa-nd-2 galaxyctl[875355]:     return complexjson.loads(self.text, **kwargs)
Apr 11 07:57:24 galaxy-qa-nd-2 galaxyctl[875355]:            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Apr 11 07:57:24 galaxy-qa-nd-2 galaxyctl[875355]:   File "/usr/lib/python3.11/json/__init__.py", line 346, in loads
Apr 11 07:57:24 galaxy-qa-nd-2 galaxyctl[875355]:     return _default_decoder.decode(s)
Apr 11 07:57:24 galaxy-qa-nd-2 galaxyctl[875355]:            ^^^^^^^^^^^^^^^^^^^^^^^^^^
Apr 11 07:57:24 galaxy-qa-nd-2 galaxyctl[875355]:   File "/usr/lib/python3.11/json/decoder.py", line 337, in decode
Apr 11 07:57:24 galaxy-qa-nd-2 galaxyctl[875355]:     obj, end = self.raw_decode(s, idx=_w(s, 0).end())
Apr 11 07:57:24 galaxy-qa-nd-2 galaxyctl[875355]:                ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Apr 11 07:57:24 galaxy-qa-nd-2 galaxyctl[875355]:   File "/usr/lib/python3.11/json/decoder.py", line 355, in raw_decode
Apr 11 07:57:24 galaxy-qa-nd-2 galaxyctl[875355]:     raise JSONDecodeError("Expecting value", s, err.value) from None
Apr 11 07:57:24 galaxy-qa-nd-2 galaxyctl[875355]: json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0)
Apr 11 07:57:24 galaxy-qa-nd-2 galaxyctl[875355]: During handling of the above exception, another exception occurred:
Apr 11 07:57:24 galaxy-qa-nd-2 galaxyctl[875355]: Traceback (most recent call last):
Apr 11 07:57:24 galaxy-qa-nd-2 galaxyctl[875355]:   File "/srv/galaxy/server/lib/galaxy/jobs/handler.py", line 1086, in __monitor
Apr 11 07:57:24 galaxy-qa-nd-2 galaxyctl[875355]:     self.__monitor_step()
Apr 11 07:57:24 galaxy-qa-nd-2 galaxyctl[875355]:   File "/srv/galaxy/server/lib/galaxy/jobs/handler.py", line 1118, in __monitor_step
Apr 11 07:57:24 galaxy-qa-nd-2 galaxyctl[875355]:     self._check_jobs(session, jobs_to_check)
Apr 11 07:57:24 galaxy-qa-nd-2 galaxyctl[875355]:   File "/srv/galaxy/server/lib/galaxy/jobs/handler.py", line 1188, in _check_jobs
Apr 11 07:57:24 galaxy-qa-nd-2 galaxyctl[875355]:     self.dispatcher.stop(job, job_wrapper)
Apr 11 07:57:24 galaxy-qa-nd-2 galaxyctl[875355]:   File "/srv/galaxy/server/lib/galaxy/jobs/handler.py", line 1267, in stop
Apr 11 07:57:24 galaxy-qa-nd-2 galaxyctl[875355]:     self.job_runners[runner_name].stop_job(job_wrapper)
Apr 11 07:57:24 galaxy-qa-nd-2 galaxyctl[875355]:   File "/srv/galaxy/server/lib/galaxy/jobs/runners/pulsar.py", line 773, in stop_job
Apr 11 07:57:24 galaxy-qa-nd-2 galaxyctl[875355]:     client.kill()
Apr 11 07:57:24 galaxy-qa-nd-2 galaxyctl[875355]:   File "/srv/galaxy/venv/lib/python3.11/site-packages/pulsar/client/client.py", line 745, in kill
Apr 11 07:57:24 galaxy-qa-nd-2 galaxyctl[875355]:     self._tes_client.cancel_task(self.job_id)
Apr 11 07:57:24 galaxy-qa-nd-2 galaxyctl[875355]:   File "/srv/galaxy/venv/lib/python3.11/site-packages/pydantictes/api.py", line 45, in cancel_task
Apr 11 07:57:24 galaxy-qa-nd-2 galaxyctl[875355]:     return TesCancelTaskResponse(**response.json())
Apr 11 07:57:24 galaxy-qa-nd-2 galaxyctl[875355]:                                    ^^^^^^^^^^^^^^^
Apr 11 07:57:24 galaxy-qa-nd-2 galaxyctl[875355]:   File "/srv/galaxy/venv/lib/python3.11/site-packages/requests/models.py", line 978, in json
Apr 11 07:57:24 galaxy-qa-nd-2 galaxyctl[875355]:     raise RequestsJSONDecodeError(e.msg, e.doc, e.pos)
Apr 11 07:57:24 galaxy-qa-nd-2 galaxyctl[875355]: requests.exceptions.JSONDecodeError: Expecting value: line 1 column 1 (char 0)
Apr 11 07:57:24 galaxy-qa-nd-2 galaxyctl[875356]: galaxy.jobs.handler DEBUG 2025-04-11 07:57:24,689 [pN:handler_1,p:875356,tN:JobHandlerStopQueue.monitor_thread] Stopping job 258 in pulsar_tes runner
Apr 11 07:57:24 galaxy-qa-nd-2 galaxyctl[875356]: galaxy.jobs.runners.pulsar DEBUG 2025-04-11 07:57:24,693 [pN:handler_1,p:875356,tN:JobHandlerStopQueue.monitor_thread] Attempt remote Pulsar kill of job with url pulsar_tes and id 67f52cf35172e48cefc64499
Apr 11 07:57:24 galaxy-qa-nd-2 galaxyctl[875356]: galaxy.jobs.handler ERROR 2025-04-11 07:57:24,715 [pN:handler_1,p:875356,tN:JobHandlerStopQueue.monitor_thread] Exception in monitor_step

TESP log:

tesp-api       | 2025-04-11 08:03:10.812 | INFO     | uvicorn.protocols.http.h11_impl:send:431 - 147.251.245.115:37333 - "POST /v1/tasks/67f52cf35172e48cefc64499%3Acancel HTTP/1.1" 200
tesp-api       | 2025-04-11 08:03:10.820 | DEBUG    | asyncio.selector_events:_read_ready__on_eof:885 - <_SelectorSocketTransport fd=12 read=polling write=<idle, bufsize=0>> received EOF
tesp-api       | 2025-04-11 08:03:11.426 | DEBUG    | asyncio.selector_events:_accept_connection:161 - <Server sockets=(<asyncio.TransportSocket fd=3, family=AddressFamily.AF_INET, type=SocketKind.SOCK_STREAM, proto=0, laddr=('0.0.0.0', 8080)>,)> got a new connection from ('147.251.245.115', 21065): <socket.socket fd=12, family=AddressFamily.AF_INET, type=SocketKind.SOCK_STREAM, proto=0, laddr=('192.168.16.4', 8080), raddr=('147.251.245.115', 21065)>

Temporary fix:
Changing job status from deleting to deleted in Galaxy SQL database.

[martenson]

xref CESNET/tesp-api#43