Modernize dictionaryutils jsonschema.RefResolver #30
Description
We have removed the dependency on gen3 by moving over the single class iceberg_tools used. dictionaryutils.DataDictionary. See https://ohsucomputationalbio.slack.com/archives/C043HPV0VMY/p1702501294219239 for rationale
However, the code we lifted over still uses a deprecated class jsonschema.RefResolver.
See the warnings displayed below.
As a low-priority task, it would be useful to modernize the resolution of schemas and possibly create a PR to the chicago dictionaryutils repo.
================================================================================ test session starts ================================================================================
platform darwin -- Python 3.9.18, pytest-7.4.0, pluggy-1.3.0
rootdir: /Users/walsbr/bmeg/iceberg-schema-tools
plugins: anyio-4.0.0, cov-4.1.0
collected 15 items
tests/integration/simplified/test_codeable_concept.py . [ 6%]
tests/integration/simplified/test_embedded_types.py . [ 13%]
tests/integration/simplified/test_identifiers.py . [ 20%]
tests/integration/simplified/test_individual_yaml.py . [ 26%]
tests/integration/simplified/test_keys.py . [ 33%]
tests/integration/simplified/test_primitive.py .. [ 46%]
tests/integration/simplified/test_quantities.py . [ 53%]
tests/integration/simplified/test_research_study_has_project.py . [ 60%]
tests/integration/simplified/test_schema.py .. [ 73%]
tests/integration/simplified/test_simplify_medication.py . [ 80%]
tests/integration/simplified/test_simplify_task.py . [ 86%]
tests/integration/simplified/test_specimen_plucked_properties.py . [ 93%]
tests/integration/simplified/test_task.py . [100%]
================================================================================= warnings summary ==================================================================================
iceberg_tools/dictionaryutils/__init__.py:7
iceberg_tools/dictionaryutils/__init__.py:7
/Users/walsbr/bmeg/iceberg-schema-tools/iceberg_tools/dictionaryutils/__init__.py:7: DeprecationWarning: jsonschema.RefResolver is deprecated as of v4.18.0, in favor of the https://github.com/python-jsonschema/referencing library, which provides more compliant referencing behavior as well as more flexible APIs for customization. A future release will remove RefResolver. Please file a feature request (on referencing) if you are missing an API for the kind of customization you need.
from jsonschema import RefResolver
-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
========================================================================== 15 passed, 2 warnings in 3.00s ===========================================================================
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