.gitignore
LICENSE
MANIFEST.in
README.md
pyproject.toml
res/evaluation_cohort/evaluation_cohort.csv
res/evaluation_cohort/fhir/curls.txt
res/evaluation_cohort/fhir/evco_fhir_condition.json
res/evaluation_cohort/fhir/evco_fhir_condition_undiagnosed_rd_case.json
res/evaluation_cohort/fhir/evco_fhir_consents.json
res/evaluation_cohort/fhir/evco_fhir_diagnostic_implication.json
res/evaluation_cohort/fhir/evco_fhir_encounter_care_pathway.json
res/evaluation_cohort/fhir/evco_fhir_family_member_history.json
res/evaluation_cohort/fhir/evco_fhir_ips_measurement_radiology.json
res/evaluation_cohort/fhir/evco_fhir_labs.json
res/evaluation_cohort/fhir/evco_fhir_observation_age_category.json
res/evaluation_cohort/fhir/evco_fhir_observation_gestation_at_birth.json
res/evaluation_cohort/fhir/evco_fhir_observation_karyotypic_sex.json
res/evaluation_cohort/fhir/evco_fhir_observation_length_of_gestation_at_birth.json
res/evaluation_cohort/fhir/evco_fhir_observation_length_of_gestation_eb51cd67a54156ee5d46263ddae5c1d3.json
res/evaluation_cohort/fhir/evco_fhir_observation_measurements_other.json
res/evaluation_cohort/fhir/evco_fhir_observation_vitalsigns.json
res/evaluation_cohort/fhir/evco_fhir_observations.json
res/evaluation_cohort/fhir/evco_fhir_patient.json
res/evaluation_cohort/fhir/evco_fhir_procedure.json
res/evaluation_cohort/fhir/evco_fhir_variant.json
res/evaluation_cohort/fhir/fhir_exporter.py
res/evaluation_cohort/phenopackets/1.json
res/evaluation_cohort/phenopackets/10.json
res/evaluation_cohort/phenopackets/2.json
res/evaluation_cohort/phenopackets/3.json
res/evaluation_cohort/phenopackets/4.json
res/evaluation_cohort/phenopackets/5.json
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res/evaluation_cohort/phenopackets/9.json
res/evaluation_cohort/redcap/2025-06-03.code-search
res/evaluation_cohort/redcap/evaluation_cohort_rarelink-cdm-linkml.json
res/evaluation_cohort/redcap/evaluation_cohort_redcap.json
res/validation/validator.ipynb
src/__init__.py
src/fsh/_build.bat
src/fsh/_build.sh
src/fsh/_gencontinuous.bat
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src/fsh/sushi-config.yaml
src/fsh/input/ignoreWarnings.txt
src/fsh/input/fsh/Bundle-rarelink-example.json
src/fsh/input/fsh/ConditionUndiagnosed_RareLink.fsh
src/fsh/input/fsh/Condition_RareLink.fsh
src/fsh/input/fsh/Consent_RareLink.fsh
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src/fsh/input/fsh/ProcedureMeasurements_RareLink.fsh
src/fsh/input/ig/surpressed-messages.json
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src/rarelink/__init__.py
src/rarelink/__main__.py
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src/rarelink/cli/fhir/__init__.py
src/rarelink/cli/fhir/export.py
src/rarelink/cli/fhir/hapi_server.py
src/rarelink/cli/fhir/restart_dockers.py
src/rarelink/cli/fhir/setup.py
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src/rarelink/cli/framework/reset.py
src/rarelink/cli/framework/status.py
src/rarelink/cli/framework/update.py
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src/rarelink/cli/phenopackets/__init__.py
src/rarelink/cli/phenopackets/export.py
src/rarelink/cli/redcap/__init__.py
src/rarelink/cli/redcap/download_records.py
src/rarelink/cli/redcap/fetch_metadata.py
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src/rarelink/cli/redcap/validate_hgvs.py
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src/rarelink/cli/setup/data_dictionary.py
src/rarelink/cli/setup/keys.py
src/rarelink/cli/setup/redcap_project.py
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src/rarelink/phenopackets/__init__.py
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src/rarelink/phenopackets/pipeline.py
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src/rarelink/phenopackets/write.py
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src/rarelink/phenopackets/adapter/multi_onset.py
src/rarelink/phenopackets/adapter/ontology_routing_adapter.py
src/rarelink/phenopackets/mappings/base_mapper.py
src/rarelink/phenopackets/mappings/disease_mapper.py
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src/rarelink/phenopackets/mappings/metadata_mapper.py
src/rarelink/phenopackets/mappings/phenotypic_feature_mapper.py
src/rarelink/phenopackets/mappings/variation_descriptor_mapper.py
src/rarelink/phenopackets/mappings/vital_status_mapper.py
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src/rarelink/phenopackets/mappings/utils/common_utils.py
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src/rarelink/rarelink_cdm/__init__.py
src/rarelink/rarelink_cdm/rarelink_cdm_datadictionary - v2_0_6.csv
src/rarelink/rarelink_cdm/mappings/__init__.py
src/rarelink/rarelink_cdm/mappings/phenopackets/__init__.py
src/rarelink/rarelink_cdm/mappings/phenopackets/combined.py
src/rarelink/rarelink_cdm/mappings/phenopackets/disease.py
src/rarelink/rarelink_cdm/mappings/phenopackets/genetics.py
src/rarelink/rarelink_cdm/mappings/phenopackets/individual.py
src/rarelink/rarelink_cdm/mappings/phenopackets/label_dicts.py
src/rarelink/rarelink_cdm/mappings/phenopackets/mapping_dicts.py
src/rarelink/rarelink_cdm/mappings/phenopackets/measurements.py
src/rarelink/rarelink_cdm/mappings/phenopackets/medical_action.py
src/rarelink/rarelink_cdm/mappings/phenopackets/ontology_paths.py
src/rarelink/rarelink_cdm/mappings/phenopackets/phenotype.py
src/rarelink/rarelink_cdm/mappings/phenopackets/resources.py
src/rarelink/rarelink_cdm/mappings/phenopackets/vitalstatus.py
src/rarelink/rarelink_cdm/mappings/redcap/__init__.py
src/rarelink/rarelink_cdm/mappings/redcap/hgvs_variables.py
src/rarelink/rarelink_cdm/mappings/redcap/map_1_formal_criteria.py
src/rarelink/rarelink_cdm/mappings/redcap/map_2_personal_information.py
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src/rarelink/rarelink_cdm/python_datamodel/rarelink_2_personal_information.py
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src/rarelink/rarelink_cdm/python_datamodel/rarelink_5_diseases.py
src/rarelink/rarelink_cdm/python_datamodel/rarelink_6_1_genetic_findings.py
src/rarelink/rarelink_cdm/python_datamodel/rarelink_6_2_phenotypic_feature.py
src/rarelink/rarelink_cdm/python_datamodel/rarelink_6_3_measurements.py
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src/rarelink/utils/code_processing.py
src/rarelink/utils/date_handling.py
src/rarelink/utils/field_access.py
src/rarelink/utils/label_fetching.py
src/rarelink/utils/mapping.py
src/rarelink/utils/redcap.py
src/rarelink/utils/schema_processing.py
src/rarelink/utils/validation.py
src/rarelink/utils/processor/__init__.py
src/rarelink/utils/processor/processor.py
tests/__init__.py
tests/conftest.py
tests/fix_imports.py
tests/acceptance/test_end_to_end.py
tests/cli/test_fhir.py
tests/cli/test_framework.py
tests/cli/test_redcap.py
tests/cli/test_setup.py
tests/integration/test_cli_integration.py
tests/integration/test_redcap_to_phenopacket_workflow.py
tests/phenopackets/__init__.py
tests/phenopackets/run_mapper_tests.py
tests/phenopackets/test_pipeline.py
tests/phenopackets/test_utils.py
tests/phenopackets/adapter/test_ontology_routing_adapter.py
tests/phenopackets/mappings/__init__.py
tests/phenopackets/mappings/test_base_mapper.py
tests/phenopackets/mappings/test_disease_mapper.py
tests/phenopackets/mappings/test_individual_mapper.py
tests/phenopackets/mappings/test_integration.py
tests/phenopackets/mappings/test_interpretation_mapper.py
tests/phenopackets/mappings/test_measurement_mapper.py
tests/phenopackets/mappings/test_medical_action_mapper.py
tests/phenopackets/mappings/test_metadata_mapper.py
tests/phenopackets/mappings/test_phenotypic_feature_mapper.py
tests/phenopackets/mappings/test_variation_descriptor_mapper.py
tests/phenopackets/mappings/test_vital_status_mapper.py
tests/phenopackets/test_data/101.json
tests/phenopackets/test_data/102.json
tests/phenopackets/test_data/103.json
tests/phenopackets/test_data/sample_records_rarelink_cdm.json
tests/phenopackets/test_data/sample_records_rarelink_cdm_1.json
tests/utils/test_code_processing.py
tests/utils/test_date_handling.py
tests/utils/test_field_access.py
tests/utils/test_processor.py
tests/utils/preprocessing/test_dates_timestamp.py
tests/utils/preprocessing/test_fetch_displays.py
tests/utils/preprocessing/test_process_redcap_code.py