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Add config option mongo_count_timeout to skip the global count per request #1757

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merged 5 commits into from Sep 27, 2023

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@ml-evs ml-evs commented Aug 24, 2023

It seems that our mongo implementation is very slow for large collections, in part because of the global structure count required for each filter. This PR adds the ability to disable that (and thus disable data_returned).

cc @eimrek,

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The diff coverage is 77.77%.

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optimade/server/config.py 93.75% <100.00%> (ø)
...made/server/entry_collections/entry_collections.py 95.83% <100.00%> (ø)
optimade/server/routers/utils.py 95.12% <ø> (ø)
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@ml-evs ml-evs force-pushed the ml-evs/add_data_returned_skip branch 2 times, most recently from 9791fb8 to 4a1beeb Compare September 18, 2023 21:23
@ml-evs ml-evs changed the title Add config option elide_data_returned to skip the global count per request Add config option mongo_count_timeout to skip the global count per request Sep 18, 2023
@ml-evs ml-evs force-pushed the ml-evs/add_data_returned_skip branch from 4a1beeb to 06d41a6 Compare September 18, 2023 21:31
@ml-evs ml-evs marked this pull request as ready for review September 22, 2023 13:30
mongo_count_timeout: int = Field(
5,
description="""Number of seconds to allow MongoDB to perform a full database count before falling back to `null`.
This operation can require a full COLLSCAN for empty queries which can be prohibitively slow if the database does not fit into the active set, hence a timeout can drastically speed-up response times.""",
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Maybe I do not fully understand what you are writing here, but I think MongoDB should know how many entries there are in a collection, so for an empty filter the query should not be slow. For a more complex query for which MongoDB cannot drastically reduce the number of entries using one of the already existing indexes this would still be a useful feature though.

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You are right, it shouldn't be slow, but previously for an empty filter we were just naively calling count_documents which does still do a full scan that can be very slow. Now, I am using estimated_document_count for this case, which uses simple collection metadata to just return the number. However for filters, it can still make use of this timeout.

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eimrek commented Sep 27, 2023

Gave this a try on the MC server for the big database, and everything works well.

See https://dev-optimade.materialscloud.org/archive/li-ion-conductors/v1/structures

Would be good to have this merged. Thanks!

However, the links:next is still broken for our APIs, but i realized it's broken also for releases 0.25.1 and 0.25.2, so it's not related to this change.

@ml-evs ml-evs added the server Issues pertaining to the example server implementation label Sep 27, 2023
@ml-evs ml-evs force-pushed the ml-evs/add_data_returned_skip branch from 06d41a6 to 13521da Compare September 27, 2023 18:22
@ml-evs ml-evs merged commit 7269566 into master Sep 27, 2023
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@ml-evs ml-evs deleted the ml-evs/add_data_returned_skip branch September 27, 2023 18:32
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3 participants