SON manipulator is deprecated in pymongo>4.0

[heuristicus]

When using ROS noetic and installing pymongo with pip3 install pymongo, you will receive a version which is above 4.0. The config manager uses an SON manipulator which was deprecated in 4.0. You can find some information at https://pymongo.readthedocs.io/en/stable/migrate-to-pymongo4.html#sonmanipulator-is-removed.

The simplest workaround is to install an earlier version of pymongo, which can be done with

pip3 install -Iv pymongo==3.12.3

3.12.3 is the latest version before 4.0.

The SON manipulator is applied in these lines:

https://github.com/mongodb/mongo-python-driver/blob/0869a5e890291ac3dd824f2b0021c7a0fb51b061/pymongo/database.py#L472-L494

One of those functions is actually called manually at

mongodb_store/mongodb_store/scripts/config_manager.py

Line 177 in 3cce5bd

existing_value = self._database._fix_outgoing(existing['value'], defaults_collection)

The changes required are to manually apply the transformation functions which exist now to each insertion/read from the database. This means that the find_one, update, insert, and maybe delete functions might need to be wrapped.