lx-data-models
lx-dtypes provides typed models for clinical research data. It checks data
against study rules and versioned medical terminology. Applications can collect
validation findings during data capture and validate records before storage or
exchange. The package also supports FHIR conversion and Django integration.
Highlights
- Reusable models for terminology, patient records, reports, and host integration.
- Versioned YAML knowledge bases with deterministic loading.
- Report-template checks for structure, coverage, and captured data.
- FHIR clinical data and terminology conversion.
- Type, test, and documentation checks in CI.
The package is in alpha. We aim to keep public imports stable. Releases
before 1.0 may include documented breaking changes.
Installation
lx-dtypes supports Python 3.12.
python -m pip install lx-dtypes
Quick start
Validate a study setup without raising for invalid input:
from lx_dtypes.models.contracts.study_setup import StudySetupDefinition
from lx_dtypes.validation import validate_contract
result = validate_contract(StudySetupDefinition, {"schema_version": "1.0"})
for issue in result.report.issues:
print(issue.code, issue.path, issue.message)
# result.value contains the typed model only when the contract is valid.
For ledger data, assess_examination(knowledge_base, payload, template_name="...") checks terminology provenance and applies the selected
template's study rules. Findings are advisory; the host decides when to require
correction. See the cross-layer validation guide
for error codes, evaluation status, and strict persistence boundaries.
Load a knowledge-base module shipped with the package:
from lx_dtypes import load_knowledge_base
knowledge_base = load_knowledge_base("report_template_examples")
print(knowledge_base.config.knowledge_base_identity)
print(sorted(knowledge_base.report_template))
Registry-backed deployments require an exact module version. The knowledge-base authoring guide explains versioning and deployment.
Provision the packaged catalog before starting a registry-backed host:
export LX_DTYPES_KB_REGISTRY=/var/lib/my-host/terminology/registry.json
lx-dtypes-kb-registry bootstrap
The command exits nonzero if the registry is invalid or a packaged identity cannot load. Hosts must treat that failure as a startup blocker.
Documentation
Follow the reader roadmap from the model overview to a working example, then choose terminology, reporting, or application integration. You can start with the topic that fits your work.
Build the documentation locally with:
python -m pip install -e ".[docs]"
make -C docs html
Development
Questions, documentation fixes, synthetic examples, and code changes are useful ways to contribute. Start with CONTRIBUTING.md for setup, checks, and pull requests. See CHANGELOG.md for release notes and SECURITY.md for vulnerability reporting.
For scoped repository navigation, start at structure.yml and follow the agent context guide.
License and citation
Distributed under the MIT License. If you use lx-dtypes in
published work, cite the project using CITATION.cff.
Metadata
Release files for lx-dtypes 0.5.5
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | Provenance | |
|---|---|---|---|---|
| lx_dtypes-0.5.5.tar.gz | 4.9 MB | Without provenance | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| lx_dtypes-0.5.5-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 6.2 MB
Release files / lx_dtypes-0.5.5.tar.gz
| Download URL | lx_dtypes-0.5.5.tar.gz |
|---|---|
| Size | 4.9 MB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
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Release files / lx_dtypes-0.5.5-py3-none-any.whl
| Download URL | lx_dtypes-0.5.5-py3-none-any.whl |
|---|---|
| Size | 1.3 MB |
| Tags | Python 3 |
|
SHA-256 checksum How to use checksums |
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No |
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twine/7.0.0 CPython/3.12.13
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Security for lx-dtypes 0.5.5
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