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LICENSE
MANIFEST.in
README.md
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submodules/tofhir/tofhir-engine/src/test/resources/test-mappings/some-folder-3/patient-mapping.json
submodules/tofhir/tofhir-engine/src/test/resources/test-mappings/some-folder-3/procedure-occurrence-mapping.json
submodules/tofhir/tofhir-engine/src/test/resources/test-schemas/some-folder-1/Ext-family-member-history.StructureDefinition.json
submodules/tofhir/tofhir-engine/src/test/resources/test-schemas/some-folder-1/Ext-other-observation.StructureDefinition.json
submodules/tofhir/tofhir-engine/src/test/resources/test-schemas/some-folder-1/Ext-patient-extra.StructureDefinition.json
submodules/tofhir/tofhir-engine/src/test/resources/test-schemas/some-folder-1/Ext-patient.StructureDefinition.json
submodules/tofhir/tofhir-engine/src/test/resources/test-schemas/some-folder-2/Ext-lab-results.StructureDefinition.json
submodules/tofhir/tofhir-engine/src/test/resources/test-schemas/some-folder-2/Ext-specimen.StructureDefinition.json
submodules/tofhir/tofhir-engine/src/test/scala/io/tofhir/OnFhirTestContainer.scala
submodules/tofhir/tofhir-engine/src/test/scala/io/tofhir/ToFhirTestSpec.scala
submodules/tofhir/tofhir-engine/src/test/scala/io/tofhir/integrationtest/KafkaSourceIntegrationTest.scala
submodules/tofhir/tofhir-engine/src/test/scala/io/tofhir/test/FhirMappingFolderRepositoryTest.scala
submodules/tofhir/tofhir-engine/src/test/scala/io/tofhir/test/FhirMappingJobManagerTest.scala
submodules/tofhir/tofhir-engine/src/test/scala/io/tofhir/test/FhirPathMappingFunctionsTest.scala
submodules/tofhir/tofhir-engine/src/test/scala/io/tofhir/test/FhirServerSourceTest.scala
submodules/tofhir/tofhir-engine/src/test/scala/io/tofhir/test/FileStreamingTest.scala
submodules/tofhir/tofhir-engine/src/test/scala/io/tofhir/test/LocalTerminologyServiceTest.scala
submodules/tofhir/tofhir-engine/src/test/scala/io/tofhir/test/SchedulingTest.scala
submodules/tofhir/tofhir-engine/src/test/scala/io/tofhir/test/SqlSourceTest.scala
submodules/tofhir/tofhir-engine/src/test/scala/io/tofhir/test/engine/data/read/FileDataSourceReaderTest.scala
submodules/tofhir/tofhir-engine/src/test/scala/io/tofhir/test/engine/data/write/FileSystemWriterTest.scala
submodules/tofhir/tofhir-engine/src/test/scala/io/tofhir/test/engine/data/write/SinkHandlerTest.scala
submodules/tofhir/tofhir-engine/src/test/scala/io/tofhir/test/engine/execution/FileStreamInputArchiverTest.scala
submodules/tofhir/tofhir-engine/src/test/scala/io/tofhir/test/engine/execution/RunningJobRegistryTest.scala
submodules/tofhir/tofhir-engine/src/test/scala/io/tofhir/test/engine/model/FhirMappingJobExecutionTest.scala
submodules/tofhir/tofhir-engine/src/test/scala/io/tofhir/test/engine/util/TerminologyMappingGeneratorTest.scala
submodules/tofhir/tofhir-rxnorm/pom.xml
submodules/tofhir/tofhir-rxnorm/src/main/scala/io/tofhir/rxnorm/PullRxNormNdcMedDetails.scala
submodules/tofhir/tofhir-rxnorm/src/main/scala/io/tofhir/rxnorm/RxNormApiClient.scala
submodules/tofhir/tofhir-rxnorm/src/main/scala/io/tofhir/rxnorm/RxNormApiFunctionLibrary.scala
submodules/tofhir/tofhir-rxnorm/src/test/scala/RxNormApiClientTest.scala
submodules/tofhir/tofhir-rxnorm/src/test/scala/RxNormApiFunctionLibraryTest.scala
submodules/tofhir/tofhir-server/api.yaml
submodules/tofhir/tofhir-server/pom.xml
submodules/tofhir/tofhir-server-common/pom.xml
submodules/tofhir/tofhir-server-common/src/main/scala/io/tofhir/server/common/config/WebServerConfig.scala
submodules/tofhir/tofhir-server-common/src/main/scala/io/tofhir/server/common/interceptor/ICORSHandler.scala
submodules/tofhir/tofhir-server-common/src/main/scala/io/tofhir/server/common/interceptor/IErrorHandler.scala
submodules/tofhir/tofhir-server-common/src/main/scala/io/tofhir/server/common/model/ToFhirError.scala
submodules/tofhir/tofhir-server-common/src/main/scala/io/tofhir/server/common/model/ToFhirRestCall.scala
submodules/tofhir/tofhir-server/src/main/resources/application.conf
submodules/tofhir/tofhir-server/src/main/resources/logback.xml
submodules/tofhir/tofhir-server/src/main/resources/version.properties
submodules/tofhir/tofhir-server/src/main/scala/io/tofhir/server/Boot.scala
submodules/tofhir/tofhir-server/src/main/scala/io/tofhir/server/ToFhirHttpServer.scala
submodules/tofhir/tofhir-server/src/main/scala/io/tofhir/server/ToFhirServer.scala
submodules/tofhir/tofhir-server/src/main/scala/io/tofhir/server/config/RedCapServiceConfig.scala
submodules/tofhir/tofhir-server/src/main/scala/io/tofhir/server/endpoint/CodeSystemEndpoint.scala
submodules/tofhir/tofhir-server/src/main/scala/io/tofhir/server/endpoint/ConceptMapEndpoint.scala
submodules/tofhir/tofhir-server/src/main/scala/io/tofhir/server/endpoint/FileSystemTreeStructureEndpoint.scala
submodules/tofhir/tofhir-server/src/main/scala/io/tofhir/server/endpoint/JobEndpoint.scala
submodules/tofhir/tofhir-server/src/main/scala/io/tofhir/server/endpoint/MappingContextEndpoint.scala
submodules/tofhir/tofhir-server/src/main/scala/io/tofhir/server/endpoint/MappingEndpoint.scala
submodules/tofhir/tofhir-server/src/main/scala/io/tofhir/server/endpoint/MetadataEndpoint.scala
submodules/tofhir/tofhir-server/src/main/scala/io/tofhir/server/endpoint/ProjectEndpoint.scala
submodules/tofhir/tofhir-server/src/main/scala/io/tofhir/server/endpoint/RedCapEndpoint.scala
submodules/tofhir/tofhir-server/src/main/scala/io/tofhir/server/endpoint/ReloadEndpoint.scala
submodules/tofhir/tofhir-server/src/main/scala/io/tofhir/server/endpoint/SchemaDefinitionEndpoint.scala
submodules/tofhir/tofhir-server/src/main/scala/io/tofhir/server/endpoint/TerminologyServiceManagerEndpoint.scala
submodules/tofhir/tofhir-server/src/main/scala/io/tofhir/server/endpoint/ToFhirServerEndpoint.scala
submodules/tofhir/tofhir-server/src/main/scala/io/tofhir/server/model/ExecuteJobTask.scala
submodules/tofhir/tofhir-server/src/main/scala/io/tofhir/server/model/FilePathNode.scala
submodules/tofhir/tofhir-server/src/main/scala/io/tofhir/server/model/ImportSchemaSettings.scala
submodules/tofhir/tofhir-server/src/main/scala/io/tofhir/server/model/InferTask.scala
submodules/tofhir/tofhir-server/src/main/scala/io/tofhir/server/model/Metadata.scala
submodules/tofhir/tofhir-server/src/main/scala/io/tofhir/server/model/Project.scala
submodules/tofhir/tofhir-server/src/main/scala/io/tofhir/server/model/TerminologySystem.scala
submodules/tofhir/tofhir-server/src/main/scala/io/tofhir/server/model/TestResourceCreationRequest.scala
submodules/tofhir/tofhir-server/src/main/scala/io/tofhir/server/model/csv/CsvHeader.scala
submodules/tofhir/tofhir-server/src/main/scala/io/tofhir/server/model/redcap/RedCapProjectConfig.scala
submodules/tofhir/tofhir-server/src/main/scala/io/tofhir/server/repository/FolderDBInitializer.scala
submodules/tofhir/tofhir-server/src/main/scala/io/tofhir/server/repository/FolderRepositoryManager.scala
submodules/tofhir/tofhir-server/src/main/scala/io/tofhir/server/repository/IRepositoryManager.scala
submodules/tofhir/tofhir-server/src/main/scala/io/tofhir/server/repository/job/IJobRepository.scala
submodules/tofhir/tofhir-server/src/main/scala/io/tofhir/server/repository/job/JobFolderRepository.scala
submodules/tofhir/tofhir-server/src/main/scala/io/tofhir/server/repository/mapping/IMappingRepository.scala
submodules/tofhir/tofhir-server/src/main/scala/io/tofhir/server/repository/mapping/ProjectMappingFolderRepository.scala
submodules/tofhir/tofhir-server/src/main/scala/io/tofhir/server/repository/mappingContext/IMappingContextRepository.scala
submodules/tofhir/tofhir-server/src/main/scala/io/tofhir/server/repository/mappingContext/MappingContextFolderRepository.scala
submodules/tofhir/tofhir-server/src/main/scala/io/tofhir/server/repository/project/IProjectList.scala
submodules/tofhir/tofhir-server/src/main/scala/io/tofhir/server/repository/project/IProjectRepository.scala
submodules/tofhir/tofhir-server/src/main/scala/io/tofhir/server/repository/project/ProjectFolderRepository.scala
submodules/tofhir/tofhir-server/src/main/scala/io/tofhir/server/repository/schema/AbstractSchemaRepository.scala
submodules/tofhir/tofhir-server/src/main/scala/io/tofhir/server/repository/schema/ISchemaRepository.scala
submodules/tofhir/tofhir-server/src/main/scala/io/tofhir/server/repository/schema/SchemaFolderRepository.scala
submodules/tofhir/tofhir-server/src/main/scala/io/tofhir/server/repository/schema/SchemaManagementUtil.scala
submodules/tofhir/tofhir-server/src/main/scala/io/tofhir/server/repository/terminology/ITerminologySystemRepository.scala
submodules/tofhir/tofhir-server/src/main/scala/io/tofhir/server/repository/terminology/TerminologySystemFolderRepository.scala
submodules/tofhir/tofhir-server/src/main/scala/io/tofhir/server/repository/terminology/codesystem/CodeSystemFolderRepository.scala
submodules/tofhir/tofhir-server/src/main/scala/io/tofhir/server/repository/terminology/codesystem/ICodeSystemRepository.scala
submodules/tofhir/tofhir-server/src/main/scala/io/tofhir/server/repository/terminology/conceptmap/ConceptMapFolderRepository.scala
submodules/tofhir/tofhir-server/src/main/scala/io/tofhir/server/repository/terminology/conceptmap/IConceptMapRepository.scala
submodules/tofhir/tofhir-server/src/main/scala/io/tofhir/server/service/ExecutionService.scala
submodules/tofhir/tofhir-server/src/main/scala/io/tofhir/server/service/JobService.scala
submodules/tofhir/tofhir-server/src/main/scala/io/tofhir/server/service/MappingContextService.scala
submodules/tofhir/tofhir-server/src/main/scala/io/tofhir/server/service/MappingService.scala
submodules/tofhir/tofhir-server/src/main/scala/io/tofhir/server/service/MetadataService.scala
submodules/tofhir/tofhir-server/src/main/scala/io/tofhir/server/service/ProjectService.scala
submodules/tofhir/tofhir-server/src/main/scala/io/tofhir/server/service/RedCapService.scala
submodules/tofhir/tofhir-server/src/main/scala/io/tofhir/server/service/ReloadService.scala
submodules/tofhir/tofhir-server/src/main/scala/io/tofhir/server/service/SchemaDefinitionService.scala
submodules/tofhir/tofhir-server/src/main/scala/io/tofhir/server/service/fhir/FileSystemTreeStructureService.scala
submodules/tofhir/tofhir-server/src/main/scala/io/tofhir/server/service/terminology/CodeSystemService.scala
submodules/tofhir/tofhir-server/src/main/scala/io/tofhir/server/service/terminology/ConceptMapService.scala
submodules/tofhir/tofhir-server/src/main/scala/io/tofhir/server/service/terminology/TerminologySystemService.scala
submodules/tofhir/tofhir-server/src/main/scala/io/tofhir/server/util/CsvUtil.scala
submodules/tofhir/tofhir-server/src/main/scala/io/tofhir/server/util/DataFrameUtil.scala
submodules/tofhir/tofhir-server/src/main/scala/io/tofhir/server/util/FileOperations.scala
submodules/tofhir/tofhir-server/src/main/scala/io/tofhir/server/util/ToFhirRejectionHandler.scala
submodules/tofhir/tofhir-server/src/test/resources/application.conf
submodules/tofhir/tofhir-server/src/test/resources/logback.xml
submodules/tofhir/tofhir-server/src/test/resources/fhir-resources/condition-resource.json
submodules/tofhir/tofhir-server/src/test/resources/fhir-resources/custom-patient-profile.json
submodules/tofhir/tofhir-server/src/test/resources/fhir-resources/custom-profiles.zip
submodules/tofhir/tofhir-server/src/test/resources/fhir-resources/fhir-profiles-missing-referenced-schemas.zip
submodules/tofhir/tofhir-server/src/test/resources/fhir-resources/invalid-condition-resource.json
submodules/tofhir/tofhir-server/src/test/resources/fhir-resources/patient-bundle.json
submodules/tofhir/tofhir-server/src/test/resources/fhir-resources/patient-resource.json
submodules/tofhir/tofhir-server/src/test/resources/file-system-structure/file1.txt
submodules/tofhir/tofhir-server/src/test/resources/file-system-structure/file2.txt
submodules/tofhir/tofhir-server/src/test/resources/file-system-structure/subdir/file3.txt
submodules/tofhir/tofhir-server/src/test/resources/redcap/instrument.csv
submodules/tofhir/tofhir-server/src/test/resources/sql/sql-source-drop.sql
submodules/tofhir/tofhir-server/src/test/resources/sql/sql-source-populate.sql
submodules/tofhir/tofhir-server/src/test/resources/streaming-parent-folder/patients/patients.csv
submodules/tofhir/tofhir-server/src/test/resources/test-data/other-observations.csv
submodules/tofhir/tofhir-server/src/test/resources/test-data/patient-gender-simple.csv
submodules/tofhir/tofhir-server/src/test/resources/test-data/patient-simple.csv
submodules/tofhir/tofhir-server/src/test/resources/test-data/patients.csv
submodules/tofhir/tofhir-server/src/test/resources/test-mapping-context/sample-unit-conversion.csv
submodules/tofhir/tofhir-server/src/test/resources/test-mapping-job/patient-mapping-job-with-two-sources.json
submodules/tofhir/tofhir-server/src/test/resources/test-mappings/other-observation-concept-map.csv
submodules/tofhir/tofhir-server/src/test/resources/test-mappings/other-observation-mapping.json
submodules/tofhir/tofhir-server/src/test/resources/test-mappings/other-observation-mapping2.json
submodules/tofhir/tofhir-server/src/test/resources/test-mappings/patient-flat-mapping.json
submodules/tofhir/tofhir-server/src/test/resources/test-mappings/patient-mapping-with-two-sources.json
submodules/tofhir/tofhir-server/src/test/resources/test-mappings/patient-mapping.json
submodules/tofhir/tofhir-server/src/test/resources/test-mappings/patient-mapping2.json
submodules/tofhir/tofhir-server/src/test/resources/test-schemas/blood-pressure-schema.json
submodules/tofhir/tofhir-server/src/test/resources/test-schemas/other-observation-schema.json
submodules/tofhir/tofhir-server/src/test/resources/test-schemas/patient-schema.json
submodules/tofhir/tofhir-server/src/test/resources/test-terminology-service/sample-code-system.csv
submodules/tofhir/tofhir-server/src/test/resources/test-terminology-service/sample-concept-map.csv
submodules/tofhir/tofhir-server/src/test/scala/io/tofhir/server/BaseEndpointTest.scala
submodules/tofhir/tofhir-server/src/test/scala/io/tofhir/server/endpoint/FhirDefinitionsEndpointTest.scala
submodules/tofhir/tofhir-server/src/test/scala/io/tofhir/server/endpoint/FileSystemTreeStructureEndpointTest.scala
submodules/tofhir/tofhir-server/src/test/scala/io/tofhir/server/endpoint/JobEndpointTest.scala
submodules/tofhir/tofhir-server/src/test/scala/io/tofhir/server/endpoint/MappingContextEndpointTest.scala
submodules/tofhir/tofhir-server/src/test/scala/io/tofhir/server/endpoint/MappingEndpointTest.scala
submodules/tofhir/tofhir-server/src/test/scala/io/tofhir/server/endpoint/MappingExecutionEndpointTest.scala
submodules/tofhir/tofhir-server/src/test/scala/io/tofhir/server/endpoint/MetadataEndpointTest.scala
submodules/tofhir/tofhir-server/src/test/scala/io/tofhir/server/endpoint/ProjectEndpointTest.scala
submodules/tofhir/tofhir-server/src/test/scala/io/tofhir/server/endpoint/ReloadingEndpointTest.scala
submodules/tofhir/tofhir-server/src/test/scala/io/tofhir/server/endpoint/SchemaEndpointTest.scala
submodules/tofhir/tofhir-server/src/test/scala/io/tofhir/server/endpoint/TerminologyServiceManagerEndpointTest.scala
submodules/tofhir/tofhir-server/src/test/scala/io/tofhir/server/endpoint/ToFhirRejectionHandlerTest.scala
submodules/tofhir/tofhir-server/src/test/scala/io/tofhir/server/service/ExecutionServiceTest.scala
submodules/tofhir/tofhir-server/src/test/scala/io/tofhir/server/util/TestUtil.scala
tests/.DS_Store
tests/__init__.py
tests/conftest.py
tests/fix_imports.py
tests/acceptance/test_end_to_end.py
tests/cdm/test_csv_update.py
tests/cdm/test_ensure_types_and_codegen.py
tests/cdm/test_normalize_and_build_schema.py
tests/cdm/test_scaffold_and_force.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/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