fix: preserve empty list/dict values in serialize() when fields specified (#146)

[rtmalikian]

Summary

Fixes a regression in v2.0.6 where save(update_fields=[...]) fails with KeyError when one of the specified fields has an empty list ([]) or empty dict ({}) value.

Root cause: serialize() always calls clean_empty_values(), which strips empty lists and dicts from the output. When save() then tries to extract the specified fields with data = {key: data[key] for key in fields}, the missing key raises KeyError.

Fix: serialize() now accepts an optional fields parameter. When provided, empty values for those specific keys are preserved after cleaning. This ensures that users can intentionally set fields to [] or {} to clear them via a partial update, without breaking the serialization pipeline for other fields.

Changes

File	Change
fhirpy/base/resource.py	Add fields parameter to serialize(); restore empty values for specified fields after clean_empty_values()
fhirpy/base/lib_async.py	Pass fields to serialize() in AsyncClient.save()
fhirpy/base/lib_sync.py	Pass fields to serialize() in SyncClient.save()
tests/test_utils.py	Add regression tests for empty list and empty dict preservation

Verification

tests/test_utils.py — 12 passed
tests/test_searchset.py — 50 passed
tests/test_lib_base.py — 50 passed
Total: 112 passed, 0 failed

Reproduction (before fix)

resource = client.resource("Patient", generalPractitioner=[practitioner1])
await resource.save()

resource["generalPractitioner"] = []
await resource.save(update_fields=["generalPractitioner"])
# KeyError: 'generalPractitioner' — empty list was stripped by clean_empty_values

After fix, the empty list is preserved for the specified field and the save succeeds.

Fixes #146

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About the Author: Raphael Malikian — Clinical AI Solutions Architect. I specialise in building and fixing AI/ML systems for healthcare, including vector databases, RAG pipelines, and clinical NLP. If you need help with your project or think I can add value to your organisation, feel free to reach out — I'd love to connect.

📧 rtmalikian@gmail.com
🔗 GitHub: https://github.com/rtmalikian
🔗 LinkedIn: http://www.linkedin.com/in/raphael-t-malikian-mbbs-bsc-hons-71075436a

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Disclosure: This code was developed with assistance from mimo-2.5-pro (Xiaomi) via Hermes Agent (Nous Research). All changes were reviewed, tested against the actual codebase, and verified for correctness.