pickle error

[edeutsch]

I just got an alert from the watchdog that ARAX generated an error. It seems okay upon manual test, so perhaps transient. the error was:

2022-04-05T21:01:02.716317 DEBUG: [] Expanding qedge e00
2022-04-05T21:01:02.716741 DEBUG: [] Modified QG for this qedge is (n00:['biolink:ChemicalEntity'] ['CHEMBL.COMPOUND:CHEMBL112'])
-['biolink:physically_interacts_with']-(n01:['biolink:Gene', 'biolink:Protein'])
2022-04-05T21:01:02.716789 DEBUG: [] For e00, pre-prune threshold is 500
2022-04-05T21:01:02.716970 DEBUG: [] Loading record of KP timeouts
2022-04-05T21:01:02.717213 DEBUG: [] Loading meta map (already exists and isn't due for a refresh)
2022-04-05T21:01:02.744132 WARNING: [] Ran into a problem getting infores:icees-dili's meta info
2022-04-05T21:01:02.748975 ERROR: [UncaughtARAXiError] An uncaught error occurred: pickle data was truncated: ['Traceback (most r
ecent call last):\n', '  File "/mnt/data/orangeboard/production/RTX/code/UI/OpenAPI/python-flask-server/openapi_server/controller
s/../../../../../ARAX/ARAXQuery/ARAX_query.py", line 715, in execute_processing_plan\n    expander.apply(response, action[\'param
eters\'], mode=mode)\n', '  File "/mnt/data/orangeboard/production/RTX/code/UI/OpenAPI/python-flask-server/openapi_server/control
lers/../../../../../ARAX/ARAXQuery/ARAX_expander.py", line 286, in apply\n    kp_selector = KPSelector(log)\n', '  File "/mnt/dat
a/orangeboard/production/RTX/code/ARAX/ARAXQuery/Expand/kp_selector.py", line 32, in __init__\n    self.meta_map = self._load_met
a_map()\n', '  File "/mnt/data/orangeboard/production/RTX/code/ARAX/ARAXQuery/Expand/kp_selector.py", line 186, in _load_meta_map
\n    meta_map = pickle.load(map_file)\n', '_pickle.UnpicklingError: pickle data was truncated\n']
INFO:werkzeug:127.0.0.1 - - [05/Apr/2022 21:01:02] "POST /api/arax/v1.2/query HTTP/1.1" 400 -
2022-04-05T21:01:03.437094 DEBUG: [] Will use asyncio to run KP queries concurrently

I wonder if maybe one process was pickling the meta_knowledge_graph cache while another was trying to read it?

not urgent. probably rarely transient.

[dkoslicki]

Still relevant @edeutsch ?

[edeutsch]

mm, probably not. I think the whole kp_selector system was rewritten with the background tasker creating the caches and the real-time queries only reading them, which hopefully avoids this kind of error. closing.