├── .coveragerc ├── .github ├── ISSUE_TEMPLATE.md ├── ISSUE_TEMPLATE │ ├── bug_report.md │ └── feature_request.md ├── dependabot.yml └── workflows │ ├── main_ci.yml │ └── publish_test_pypi.yml ├── .gitignore ├── .pre-commit-config.yaml ├── CHANGELOG.md ├── LICENSE ├── README.md ├── benchmarks ├── README.md ├── benchmark_clients.py ├── benchmark_servers.py ├── configs │ ├── linux4health │ │ ├── bulkdata │ │ │ ├── in │ │ │ │ └── Patient_1.ndjson │ │ │ └── out │ │ │ │ └── .empty │ │ ├── config │ │ │ └── default │ │ │ │ ├── extension-search-parameters.json │ │ │ │ └── fhir-server-config.json │ │ ├── configDropins │ │ │ ├── datasources.xml │ │ │ └── unsafe.xml │ │ ├── openapi.json │ │ └── userlib │ │ │ └── .empty │ └── postgres │ │ └── init │ │ └── users.sql ├── docker-compose.yml └── results │ ├── 10000-generate_results.json │ ├── query-results.json │ └── query_plot.png ├── docs ├── add.md ├── api.md ├── assets │ └── logo.png ├── benchmark.md ├── connect.md ├── delete.md ├── ds.md ├── index.md ├── logo │ ├── kindling_header.png │ ├── kindling_logo.jpeg │ ├── kindling_logo_no_bg.png │ └── kindling_logo_small.png ├── query.md ├── transfer.md └── update.md ├── examples ├── assets │ ├── kindling_header.png │ ├── query_plot.png │ ├── resource_graphs.png │ └── upload_graph.png ├── cord_data_to_fhir.py ├── demo.ipynb ├── docker-compose.yml ├── examples.ipynb └── query_response.json ├── fhir_kindling ├── __init__.py ├── benchmark │ ├── __init__.py │ ├── bench.py │ ├── constants.py │ ├── data.py │ ├── figures.py │ └── results.py ├── fhir_query │ ├── __init__.py │ ├── base.py │ ├── query_async.py │ ├── query_parameters.py │ ├── query_response.py │ └── query_sync.py ├── fhir_server │ ├── __init__.py │ ├── auth.py │ ├── fhir_server.py │ ├── server_responses.py │ ├── summary.py │ ├── transactions.py │ └── transfer.py ├── figures │ ├── __init__.py │ ├── resource_plots.py │ └── summary.py ├── generators │ ├── __init__.py │ ├── base.py │ ├── dataset.py │ ├── field_generator.py │ ├── patient.py │ ├── resource_generator.py │ └── time_series_generator.py ├── privacy │ ├── __init__.py │ └── k_anonymity.py ├── serde │ ├── __init__.py │ ├── flatten.py │ └── json.py ├── tests │ ├── __init__.py │ ├── conftest.py │ ├── server │ │ ├── __init__.py │ │ └── test_transfer.py │ ├── test_auth.py │ ├── test_benchmark.py │ ├── test_date_util.py │ ├── test_fhir_query.py │ ├── test_fhir_server.py │ ├── test_generators.py │ ├── test_plots.py │ ├── test_privacy.py │ ├── test_serialization.py │ └── test_util.py └── util │ ├── __init__.py │ ├── date_utils.py │ ├── references.py │ ├── resources.py │ └── retry_transport.py ├── mkdocs.yml ├── poetry.lock ├── pyproject.toml └── testing ├── docker-compose.yml ├── get_diverse_bundle.py ├── prefill.py └── realm.json /.coveragerc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/migraf/fhir-kindling/HEAD/.coveragerc 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