Scout: pymongo.errors.DocumentTooLarge: 'findAndModify' command document too large error

[northwestwitch]

021-05-17 10:51:16,241 - scout.server.app - ERROR: Exception on /cust003/2015/variants [GET] [in /home/hiseq.clinical/miniconda/envs/prod/lib/python3.6/site-packages/flask/app.py:1892]
Traceback (most recent call last):
File "/home/hiseq.clinical/miniconda/envs/prod/lib/python3.6/site-packages/flask/app.py", line 2447, in wsgi_app
response = self.full_dispatch_request()
File "/home/hiseq.clinical/miniconda/envs/prod/lib/python3.6/site-packages/flask/app.py", line 1952, in full_dispatch_request
rv = self.handle_user_exception(e)
File "/home/hiseq.clinical/miniconda/envs/prod/lib/python3.6/site-packages/flask/app.py", line 1821, in handle_user_exception
reraise(exc_type, exc_value, tb)
File "/home/hiseq.clinical/miniconda/envs/prod/lib/python3.6/site-packages/flask/_compat.py", line 39, in reraise
raise value
File "/home/hiseq.clinical/miniconda/envs/prod/lib/python3.6/site-packages/flask/app.py", line 1950, in full_dispatch_request
rv = self.dispatch_request()
File "/home/hiseq.clinical/miniconda/envs/prod/lib/python3.6/site-packages/flask/app.py", line 1936, in dispatch_request
return self.view_functionsrule.endpoint
File "/home/hiseq.clinical/SERVER/apps/scout/git/scout/scout/server/utils.py", line 26, in decorated_function
context = func(args, *kwargs)
File "/home/hiseq.clinical/SERVER/apps/scout/git/scout/scout/server/blueprints/variants/views.py", line 126, in variants
data = controllers.variants(store, institute_obj, case_obj, variants_query, result_size, page)
File "/home/hiseq.clinical/SERVER/apps/scout/git/scout/scout/server/blueprints/variants/controllers.py", line 102, in variants
store, institute_obj, case_obj, variant_obj, update=True, genome_build=genome_build
File "/home/hiseq.clinical/SERVER/apps/scout/git/scout/scout/server/blueprints/variants/controllers.py", line 335, in parse_variant
variant_obj = store.update_variant(variant_obj)
File "/home/hiseq.clinical/SERVER/apps/scout/git/scout/scout/adapter/mongo/variant_loader.py", line 51, in update_variant
return_document=pymongo.ReturnDocument.AFTER,
File "/home/hiseq.clinical/miniconda/envs/prod/lib/python3.6/site-packages/pymongo/collection.py", line 3123, in find_one_and_replace
hint=hint, session=session, **kwargs)
File "/home/hiseq.clinical/miniconda/envs/prod/lib/python3.6/site-packages/pymongo/collection.py", line 2972, in __find_and_modify
write_concern.acknowledged, _find_and_modify, session)
File "/home/hiseq.clinical/miniconda/envs/prod/lib/python3.6/site-packages/pymongo/mongo_client.py", line 1498, in _retryable_write
return self._retry_with_session(retryable, func, s, None)
File "/home/hiseq.clinical/miniconda/envs/prod/lib/python3.6/site-packages/pymongo/mongo_client.py", line 1384, in _retry_with_session
return self._retry_internal(retryable, func, session, bulk)
File "/home/hiseq.clinical/miniconda/envs/prod/lib/python3.6/site-packages/pymongo/mongo_client.py", line 1416, in _retry_internal
return func(session, sock_info, retryable)
File "/home/hiseq.clinical/miniconda/envs/prod/lib/python3.6/site-packages/pymongo/collection.py", line 2966, in _find_and_modify
user_fields=_FIND_AND_MODIFY_DOC_FIELDS)
File "/home/hiseq.clinical/miniconda/envs/prod/lib/python3.6/site-packages/pymongo/collection.py", line 253, in _command
user_fields=user_fields)
File "/home/hiseq.clinical/miniconda/envs/prod/lib/python3.6/site-packages/pymongo/pool.py", line 699, in command
self._raise_connection_failure(error)
File "/home/hiseq.clinical/miniconda/envs/prod/lib/python3.6/site-packages/pymongo/pool.py", line 694, in command
exhaust_allowed=exhaust_allowed)
File "/home/hiseq.clinical/miniconda/envs/prod/lib/python3.6/site-packages/pymongo/network.py", line 136, in command
name, size, max_bson_size + message._COMMAND_OVERHEAD)
File "/home/hiseq.clinical/miniconda/envs/prod/lib/python3.6/site-packages/pymongo/message.py", line 1092, in _raise_document_too_large
raise DocumentTooLarge("%r command document too large" % (operation,))
pymongo.errors.DocumentTooLarge: 'findAndModify' command document too large

[northwestwitch]

What is this error, do we have documents bigger than 16 Mb?

[dnil]

Hm, an old migrated case?

[northwestwitch]

To reproduce, go to this case: https://scout.scilifelab.se/cust003/2015/variants and deselect all gene panels from the filter when filtering for variants

[northwestwitch]

Hm, an old migrated case?

yes

[dnil]

Its in the compound update I guess - something that changed in how we represent them that causes too much stuff to get pulled?

[northwestwitch]

The thing is we haven't deployed the compound update yet 🤔

[dnil]

Well, no, not the latest, but we still run that build compounds part for cases like the "first" time they open, since way back when.

[northwestwitch]

At least the same case is on stage, since it's old!

[northwestwitch]

Loading of variants page on the stage case fails when updating this specific variant: aa472e7a595ae25d0c499ced46653cb4