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Merge pull request #15 from fbraza/fix/issue-8-comprehensive-type-hints
Fix type hint issues with TypedDict approach
2 parents 141b1c6 + 7b888e1 commit d8a9eb4

29 files changed

+830
-810
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‎.github/workflows/claude-code-review.yml‎

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# github.event.pull_request.user.login == 'external-contributor' ||
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# github.event.pull_request.user.login == 'new-developer' ||
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# github.event.pull_request.author_association == 'FIRST_TIME_CONTRIBUTOR'
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runs-on: ubuntu-latest
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permissions:
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contents: read
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pull-requests: read
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issues: read
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id-token: write
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steps:
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- name: Checkout repository
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uses: actions/checkout@v4
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# Optional: Specify model (defaults to Claude Sonnet 4, uncomment for Claude Opus 4)
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# model: "claude-opus-4-20250514"
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# Direct prompt for automated review (no @claude mention needed)
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direct_prompt: |
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Please review this pull request and provide feedback on:
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- Performance considerations
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- Security concerns
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- Test coverage
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Be constructive and helpful in your feedback.
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# Optional: Use sticky comments to make Claude reuse the same comment on subsequent pushes to the same PR
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# use_sticky_comment: true
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# Optional: Customize review based on file types
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# direct_prompt: |
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# Review this PR focusing on:
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# - For TypeScript files: Type safety and proper interface usage
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# - For API endpoints: Security, input validation, and error handling
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# - For React components: Performance, accessibility, and best practices
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# - For tests: Coverage, edge cases, and test quality
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# Optional: Different prompts for different authors
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# direct_prompt: |
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# ${{ github.event.pull_request.author_association == 'FIRST_TIME_CONTRIBUTOR' &&
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# ${{ github.event.pull_request.author_association == 'FIRST_TIME_CONTRIBUTOR' &&
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# 'Welcome! Please review this PR from a first-time contributor. Be encouraging and provide detailed explanations for any suggestions.' ||
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# 'Please provide a thorough code review focusing on our coding standards and best practices.' }}
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# Optional: Add specific tools for running tests or linting
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# allowed_tools: "Bash(npm run test),Bash(npm run lint),Bash(npm run typecheck)"
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# Optional: Skip review for certain conditions
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# if: |
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# !contains(github.event.pull_request.title, '[skip-review]') &&
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# !contains(github.event.pull_request.title, '[WIP]')
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‎specs/coding_style.md‎

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@@ -109,4 +109,4 @@ When faced with coding choices, ask:
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5. **Does this follow our established conventions?**
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6. **Is this optimized for readability?**
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The answer to all these questions should be "yes" for beautiful Python code.
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The answer to all these questions should be "yes" for beautiful Python code.

‎tests/inputs/score2/test__input__patient_25.json‎

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{
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"metadata": {
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"patient_id": "P024-2024-024",
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"sex": "female",
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"timestamp": "2024-07-04T13:45:00Z",
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"test_date": "2024-07-04",
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"laboratory": "NHANES Reference Labs"
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},
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"raw_biomarkers": {
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"age_years": {
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"value": 50,
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"unit": "years"
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"metadata": {
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"patient_id": "P024-2024-024",
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"sex": "female",
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"timestamp": "2024-07-04T13:45:00Z",
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"test_date": "2024-07-04",
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"laboratory": "NHANES Reference Labs"
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},
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"smoking_yes_no": {
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"value": true,
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"unit": "yes/no"
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},
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"systolic_blood_pressure_mmhg": {
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"value": 140,
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"unit": "mmHg"
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},
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"total_cholesterol_mmol_l": {
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"value": 6.3,
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"unit": "mmol/L"
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},
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"hdl_cholesterol_mmol_l": {
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"value": 1.4,
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"unit": "mmol/L"
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},
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"is_male_yes_no": {
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"value": false,
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"unit": "yes/no"
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"raw_biomarkers": {
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"age_years": {
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"value": 50,
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"unit": "years"
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},
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"smoking_yes_no": {
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"value": true,
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"unit": "yes/no"
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},
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"systolic_blood_pressure_mmhg": {
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"value": 140,
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"unit": "mmHg"
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},
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"total_cholesterol_mmol_l": {
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"value": 6.3,
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"unit": "mmol/L"
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},
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"hdl_cholesterol_mmol_l": {
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"value": 1.4,
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"unit": "mmol/L"
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},
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"is_male_yes_no": {
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"value": false,
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"unit": "yes/no"
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}
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}
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}
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}

‎tests/inputs/score2/test__input__patient_26.json‎

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{
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"metadata": {
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"patient_id": "P024-2024-024",
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"sex": "male",
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"timestamp": "2024-07-04T13:45:00Z",
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"test_date": "2024-07-04",
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"laboratory": "NHANES Reference Labs"
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},
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"raw_biomarkers": {
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"age_years": {
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"value": 50,
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"unit": "years"
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"metadata": {
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"patient_id": "P024-2024-024",
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"sex": "male",
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"timestamp": "2024-07-04T13:45:00Z",
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"test_date": "2024-07-04",
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"laboratory": "NHANES Reference Labs"
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},
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"smoking_yes_no": {
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"value": true,
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"unit": "yes/no"
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},
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"systolic_blood_pressure_mmhg": {
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"value": 140,
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"unit": "mmHg"
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},
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"total_cholesterol_mmol_l": {
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"value": 6.3,
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"unit": "mmol/L"
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},
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"hdl_cholesterol_mmol_l": {
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"value": 1.4,
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"unit": "mmol/L"
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},
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"is_male_yes_no": {
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"value": true,
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"unit": "yes/no"
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"raw_biomarkers": {
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"age_years": {
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"value": 50,
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"unit": "years"
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},
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"smoking_yes_no": {
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"value": true,
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"unit": "yes/no"
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},
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"systolic_blood_pressure_mmhg": {
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"value": 140,
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"unit": "mmHg"
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},
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"total_cholesterol_mmol_l": {
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"value": 6.3,
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"unit": "mmol/L"
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},
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"hdl_cholesterol_mmol_l": {
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"value": 1.4,
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"unit": "mmol/L"
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},
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"is_male_yes_no": {
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"value": true,
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"unit": "yes/no"
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}
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}
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}
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}

‎tests/inputs/score2/test__input__patient_27.json‎

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{
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"metadata": {
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"patient_id": "P027-2024-027",
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"sex": "female",
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"timestamp": "2024-07-04T14:00:00Z",
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"test_date": "2024-07-04",
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"laboratory": "NHANES Reference Labs"
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},
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"raw_biomarkers": {
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"age_years": {
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"value": 55,
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"unit": "years"
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"metadata": {
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"patient_id": "P027-2024-027",
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"sex": "female",
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"timestamp": "2024-07-04T14:00:00Z",
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"test_date": "2024-07-04",
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"laboratory": "NHANES Reference Labs"
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},
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"smoking_yes_no": {
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"value": false,
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"unit": "yes/no"
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},
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"systolic_blood_pressure_mmhg": {
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"value": 125,
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"unit": "mmHg"
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},
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"total_cholesterol_mmol_l": {
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"value": 5.2,
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"unit": "mmol/L"
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},
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"hdl_cholesterol_mmol_l": {
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"value": 1.6,
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"unit": "mmol/L"
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},
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"is_male_yes_no": {
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"value": false,
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"unit": "yes/no"
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"raw_biomarkers": {
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"age_years": {
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"value": 55,
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"unit": "years"
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},
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"smoking_yes_no": {
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"value": false,
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"unit": "yes/no"
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},
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"systolic_blood_pressure_mmhg": {
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"value": 125,
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"unit": "mmHg"
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},
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"total_cholesterol_mmol_l": {
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"value": 5.2,
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"unit": "mmol/L"
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},
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"hdl_cholesterol_mmol_l": {
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"value": 1.6,
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"unit": "mmol/L"
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},
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"is_male_yes_no": {
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"value": false,
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"unit": "yes/no"
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}
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}
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}
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}
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}

‎tests/inputs/score2/test__input__patient_28.json‎

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{
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"metadata": {
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"patient_id": "P028-2024-028",
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"sex": "male",
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"timestamp": "2024-07-04T14:15:00Z",
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"test_date": "2024-07-04",
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"laboratory": "NHANES Reference Labs"
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},
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"raw_biomarkers": {
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"age_years": {
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"value": 45,
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"unit": "years"
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"metadata": {
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"patient_id": "P028-2024-028",
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"sex": "male",
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"timestamp": "2024-07-04T14:15:00Z",
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"test_date": "2024-07-04",
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"laboratory": "NHANES Reference Labs"
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},
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"smoking_yes_no": {
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"value": false,
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"unit": "yes/no"
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},
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"systolic_blood_pressure_mmhg": {
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"value": 130,
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"unit": "mmHg"
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},
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"total_cholesterol_mmol_l": {
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"value": 5.8,
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"unit": "mmol/L"
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},
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"hdl_cholesterol_mmol_l": {
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"value": 1.3,
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"unit": "mmol/L"
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},
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"is_male_yes_no": {
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"value": true,
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"unit": "yes/no"
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"raw_biomarkers": {
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"age_years": {
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"value": 45,
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"unit": "years"
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},
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"smoking_yes_no": {
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"value": false,
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"unit": "yes/no"
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},
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"systolic_blood_pressure_mmhg": {
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"value": 130,
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"unit": "mmHg"
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},
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"total_cholesterol_mmol_l": {
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"value": 5.8,
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"unit": "mmol/L"
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},
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"hdl_cholesterol_mmol_l": {
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"value": 1.3,
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"unit": "mmol/L"
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},
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"is_male_yes_no": {
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"value": true,
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"unit": "yes/no"
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}
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}
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}
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}
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}

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