Performance of referencing library vs deprecated jsonschema.RefResolver is very bad when there are a lot of references in schema

Hello!

I have a library that formats scientific data into a JSON schema called the Allotrope Standard Model (ASM)

The validation schemas are fairly large and complicated compared to other schemas I've seen in discussion boards, and are very modular, meaning there are a lot of references. In allotropy we store the ASM schemas directly, and remove all remote references, replacing them with local references under $defs.

We are finding that validating against the schemas using jsonschema version 4.18.0 takes ~20x longer than 4.17.0.

As a concrete example:

Validating this data: https://raw.githubusercontent.com/Benchling-Open-Source/allotropy/refs/heads/main/tests/parsers/moldev_softmax_pro/testdata/MD_SMP_luminescence_endpoint_example08.json

Against this schema: https://github.com/Benchling-Open-Source/allotropy/blob/main/src/allotropy/allotrope/schemas/adm/plate-reader/REC/2024/06/plate-reader.schema.json

takes ~3.5s on 4.17.0 and ~55s on 4.18.0

This translates to a runtime for all 26 tests in tests/parsers/moldev_softmax_pro of ~30s in 4.17.0 to ~6m in 4.18.0

Riproduci il caso di validazione segnalato usando i dati di test e lo schema di plate-reader collegati, confrontando jsonschema 4.17.0 con 4.18.0. Inizia da tests/parsers/moldev_softmax_pro e dal suo runtime di 26 test, quindi segui il percorso di referenziamento e validazione per identificare la regressione. Il lavoro è concluso quando la causa è isolata e lo schema con riferimenti grandi non mostra più il rallentamento segnalato.