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@aslgraefe
aslgraefe committed Oct 22, 2024
1 parent dc315b8 commit c6ce4b4
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Showing 3 changed files with 3 additions and 3 deletions.
2 changes: 1 addition & 1 deletion submodules/phenopacket_mapper
Submodule phenopacket_mapper updated 3 files
+27 −2 src/phenopacket_mapper/data_standards/data_model.py
+2 −7 src/phenopacket_mapper/mapping/mapper.py
+62 −0 tests/utils/test_recursive_collect_all_members_data_model.py
2 changes: 1 addition & 1 deletion submodules/rd-cdm
Submodule rd-cdm updated 1 files
+ − docs/_static/v2_0_0_dev0/figure1_rd_cdm.jpeg
2 changes: 1 addition & 1 deletion submodules/tofhir
Submodule tofhir updated 95 files
+23 −10 README.md
+2 −2 docker/engine/build.sh
+4 −4 docker/fluentd/Dockerfile
+3 −0 docker/fluentd/build.sh
+3 −3 docker/kibana/Dockerfile
+3 −0 docker/kibana/build.sh
+1 −1 docker/kibana/exports/dashboards.ndjson
+1 −1 docker/kibana/exports/required_fields_index_template.json
+6 −2 tofhir-common/src/main/scala/io/tofhir/common/model/SchemaDefinition.scala
+1 −0 tofhir-common/src/main/scala/io/tofhir/common/util/SchemaUtil.scala
+1 −1 tofhir-engine/src/main/scala/io/tofhir/engine/cli/CommandLineInterface.scala
+3 −3 tofhir-engine/src/main/scala/io/tofhir/engine/cli/command/Load.scala
+8 −16 tofhir-engine/src/main/scala/io/tofhir/engine/cli/command/Run.scala
+8 −8 tofhir-engine/src/main/scala/io/tofhir/engine/cli/command/Stop.scala
+10 −10 tofhir-engine/src/main/scala/io/tofhir/engine/data/read/BaseDataSourceReader.scala
+6 −6 tofhir-engine/src/main/scala/io/tofhir/engine/data/read/FhirServerDataSourceReader.scala
+86 −95 tofhir-engine/src/main/scala/io/tofhir/engine/data/read/FileDataSourceReader.scala
+10 −10 tofhir-engine/src/main/scala/io/tofhir/engine/data/read/KafkaSourceReader.scala
+11 −10 tofhir-engine/src/main/scala/io/tofhir/engine/data/read/SourceHandler.scala
+10 −20 tofhir-engine/src/main/scala/io/tofhir/engine/data/read/SqlSourceReader.scala
+9 −8 tofhir-engine/src/main/scala/io/tofhir/engine/data/write/FhirRepositoryWriter.scala
+23 −23 tofhir-engine/src/main/scala/io/tofhir/engine/data/write/FileSystemWriter.scala
+15 −15 tofhir-engine/src/main/scala/io/tofhir/engine/data/write/SinkHandler.scala
+31 −31 tofhir-engine/src/main/scala/io/tofhir/engine/execution/RunningJobRegistry.scala
+15 −13 tofhir-engine/src/main/scala/io/tofhir/engine/execution/log/ExecutionLogger.scala
+71 −32 tofhir-engine/src/main/scala/io/tofhir/engine/execution/processing/ErroneousRecordWriter.scala
+16 −16 tofhir-engine/src/main/scala/io/tofhir/engine/execution/processing/FileStreamInputArchiver.scala
+13 −13 tofhir-engine/src/main/scala/io/tofhir/engine/mapping/FhirMappingService.scala
+45 −31 tofhir-engine/src/main/scala/io/tofhir/engine/mapping/MappingTaskExecutor.scala
+59 −42 tofhir-engine/src/main/scala/io/tofhir/engine/mapping/job/FhirMappingJobManager.scala
+2 −1 tofhir-engine/src/main/scala/io/tofhir/engine/mapping/schema/SchemaConverter.scala
+2 −0 tofhir-engine/src/main/scala/io/tofhir/engine/model/FhirMapping.scala
+30 −18 tofhir-engine/src/main/scala/io/tofhir/engine/model/FhirMappingJob.scala
+17 −39 tofhir-engine/src/main/scala/io/tofhir/engine/model/FhirMappingJobExecution.scala
+6 −5 tofhir-engine/src/main/scala/io/tofhir/engine/model/FhirMappingJobResult.scala
+168 −39 tofhir-engine/src/main/scala/io/tofhir/engine/model/FhirMappingResult.scala
+17 −63 tofhir-engine/src/main/scala/io/tofhir/engine/model/FhirMappingTask.scala
+6 −12 tofhir-engine/src/main/scala/io/tofhir/engine/model/FhirSinkSettings.scala
+19 −3 tofhir-engine/src/main/scala/io/tofhir/engine/util/FhirMappingJobFormatter.scala
+12 −10 tofhir-engine/src/main/scala/io/tofhir/engine/util/SparkUtil.scala
+23 −0 tofhir-engine/src/main/scala/io/tofhir/engine/util/TimeUtil.scala
+1 −0 tofhir-engine/src/main/scala/io/tofhir/engine/util/redcap/RedCapUtil.scala
+3 −2 tofhir-engine/src/test/resources/patient-mapping-job-with-two-sources.json
+4 −2 tofhir-engine/src/test/resources/streaming-job-example.json
+1 −0 tofhir-engine/src/test/resources/test-mapping-job-kafka.json
+6 −2 tofhir-engine/src/test/resources/test-mappingjob-using-services.json
+6 −2 tofhir-engine/src/test/resources/test-mappingjob.json
+74 −0 tofhir-engine/src/test/resources/test-mappings/patient-mapping-with-draft.json
+36 −0 tofhir-engine/src/test/resources/test-mappings/patient-mapping-with-json-patch.json
+2 −0 tofhir-engine/src/test/resources/test-schedule-mappingjob.json
+3 −0 tofhir-engine/src/test/resources/test-sql-mappingjob.json
+4 −1 tofhir-engine/src/test/scala/io/tofhir/integrationtest/KafkaSourceIntegrationTest.scala
+113 −78 tofhir-engine/src/test/scala/io/tofhir/test/FhirMappingJobManagerTest.scala
+9 −4 tofhir-engine/src/test/scala/io/tofhir/test/FhirServerSourceTest.scala
+10 −6 tofhir-engine/src/test/scala/io/tofhir/test/FileStreamingTest.scala
+15 −10 tofhir-engine/src/test/scala/io/tofhir/test/SqlSourceTest.scala
+103 −88 tofhir-engine/src/test/scala/io/tofhir/test/engine/data/read/FileDataSourceReaderTest.scala
+137 −108 tofhir-engine/src/test/scala/io/tofhir/test/engine/data/write/FileSystemWriterTest.scala
+2 −2 tofhir-engine/src/test/scala/io/tofhir/test/engine/data/write/SinkHandlerTest.scala
+44 −44 tofhir-engine/src/test/scala/io/tofhir/test/engine/execution/FileStreamInputArchiverTest.scala
+6 −6 tofhir-engine/src/test/scala/io/tofhir/test/engine/execution/RunningJobRegistryTest.scala
+5 −5 tofhir-engine/src/test/scala/io/tofhir/test/engine/model/FhirMappingJobExecutionTest.scala
+772 −319 tofhir-server/api.yaml
+10 −9 tofhir-server/src/main/scala/io/tofhir/server/endpoint/FhirDefinitionsEndpoint.scala
+1 −1 tofhir-server/src/main/scala/io/tofhir/server/endpoint/FileSystemTreeStructureEndpoint.scala
+7 −7 tofhir-server/src/main/scala/io/tofhir/server/endpoint/JobEndpoint.scala
+3 −3 tofhir-server/src/main/scala/io/tofhir/server/model/ExecuteJobTask.scala
+3 −0 tofhir-server/src/main/scala/io/tofhir/server/model/ProfileInfo.scala
+1 −2 tofhir-server/src/main/scala/io/tofhir/server/model/TestResourceCreationRequest.scala
+7 −1 tofhir-server/src/main/scala/io/tofhir/server/repository/job/JobFolderRepository.scala
+1 −1 tofhir-server/src/main/scala/io/tofhir/server/repository/mapping/ProjectMappingFolderRepository.scala
+22 −15 tofhir-server/src/main/scala/io/tofhir/server/repository/schema/SchemaFolderRepository.scala
+32 −0 tofhir-server/src/main/scala/io/tofhir/server/repository/schema/SchemaManagementUtil.scala
+40 −31 tofhir-server/src/main/scala/io/tofhir/server/service/ExecutionService.scala
+4 −3 tofhir-server/src/main/scala/io/tofhir/server/service/SchemaDefinitionService.scala
+18 −26 tofhir-server/src/main/scala/io/tofhir/server/service/fhir/FhirDefinitionsService.scala
+29 −6 tofhir-server/src/main/scala/io/tofhir/server/service/fhir/FileSystemTreeStructureService.scala
+12 −6 tofhir-server/src/main/scala/io/tofhir/server/service/fhir/SimpleStructureDefinitionService.scala
+9 −9 tofhir-server/src/main/scala/io/tofhir/server/util/DataFrameUtil.scala
+2 −1 tofhir-server/src/main/scala/io/tofhir/server/util/FileOperations.scala
+2 −0 tofhir-server/src/test/resources/test-data/patient-gender-simple.csv
+2 −0 tofhir-server/src/test/resources/test-data/patient-simple.csv
+51 −0 tofhir-server/src/test/resources/test-mapping-job/patient-mapping-job-with-two-sources.json
+42 −0 tofhir-server/src/test/resources/test-mappings/patient-mapping-with-two-sources.json
+1 −0 tofhir-server/src/test/resources/test-schemas/other-observation-schema.json
+1 −0 tofhir-server/src/test/resources/test-schemas/patient-schema.json
+1 −1 tofhir-server/src/test/scala/io/tofhir/server/endpoint/FhirDefinitionsEndpointTest.scala
+8 −11 tofhir-server/src/test/scala/io/tofhir/server/endpoint/FileSystemTreeStructureEndpointTest.scala
+26 −5 tofhir-server/src/test/scala/io/tofhir/server/endpoint/JobEndpointTest.scala
+3 −2 tofhir-server/src/test/scala/io/tofhir/server/endpoint/MappingEndpointTest.scala
+118 −45 tofhir-server/src/test/scala/io/tofhir/server/endpoint/MappingExecutionEndpointTest.scala
+1 −0 tofhir-server/src/test/scala/io/tofhir/server/endpoint/ProjectEndpointTest.scala
+21 −9 tofhir-server/src/test/scala/io/tofhir/server/endpoint/SchemaEndpointTest.scala
+2 −1 tofhir-server/src/test/scala/io/tofhir/server/endpoint/TerminologyServiceManagerEndpointTest.scala
+5 −3 tofhir-server/src/test/scala/io/tofhir/server/service/ExecutionServiceTest.scala

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