NEDSS-DataIngestion

Data Ingestion for Modernization of NEDSS Project by Enquizit

Running Application inside Docker

• Requirement
  • Java 17
    • Docker

      • Gradle

        • Building application with Docker
          • Create env file on the top directory and name it as dataingestion.env. Update the content below with appropriate value

              DI_DBSERVER=value
            
              DI_DBNAME=value
            
              DI_USERNAME=value
            
              DI_PASSWORD=value
            
              DI_NBS_DBSERVER=value
            
              DI_NBS_DBNAME=value
            
              DI_NBS_DBUSER=value
            
              DI_NBS_DBPASSWORD=value
              
              DI_ODSE_DBNAME=value
            
              DI_LOG_PATH=value
            
              DI_AUTH_URI=value
            
              DI_SFTP_ENABLED=value
            
              DI_SFTP_HOST=value
            
              DI_SFTP_USER=value
            
              DI_SFTP_PWD=value
            
              DI_SERVER_HOST=value
            

          - Run "docker-compose up -d"
          - If encounter gradle exception such as missing wrapper then run the following command
            - "gradle wrapper"
          
          

• Build project with gradle (no docker)
  • ./gradlew :hl7-parser:build
  • ./gradlew :data-ingestion-service:build
  • ./gradlew build

Building Docker image for EKS (1)

• If you are on Mac OS Environnment, look into Docker Buildx, so linux image can be built
• This example assume local machine run Mac OS.
• Run "docker buildx build --platform linux/amd64 -t <DOCKER_REPOS>/<IMAGE_NAME>:<VERSION> -f data-ingestion-service/Dockerfile . --push"
  • This command look for Dockerfile inside data-ingestion-service directory and build image from the top level of the project's hierarchy

Deploy Docker image on EKS (2)

• These steps assume EKS cluster already exist and running, and it is being manage by Helm Charts
• Run "helm upgrade --install dataingestion-service -f ./dataingestion-service/values-dev.yaml --set jdbc.dbserver='VALUE',jdbc.dbname='VALUE',jdbc.username='VALUE',jdbc.password='VALUE',jdbc.nbs.dbserver='VALUE',jdbc.nbs.dbname='VALUE',jdbc.nbs.username='VALUE',jdbc.nbs.password='VALUE',kafka.cluster='VALUE' dataingestion-service"
  • What this command does is create new if not service not exist and update existing one if it exists.
  • values-dev.yaml: indicate value file, helm charts pull values such as enviroment variable from this file.
  • --set jdb.dbserver='VALUE': argument to pass value into enviroment variable, this value is defined in values-dev.yaml.
  • --set image.repository='VALUE': image repos, say if using registry other than docker hub. Ex: ECR
  • Docker Image need to be specify in values-dev.yaml
  • For Helm Chart and EKS configuration, please refer to this NEDSS-Helm
• Other useful commands
  • helm delete <SERVICE-NAME>: delete service
  • kubectl exec -it <POD-ID> -- /bin/bash : access pod environment
  • kubectl get pods
  • kubectl describe pod <POD-ID>: get pod info, useful to inspect configuration and debug
  • kubectl logs <POD-ID>

Unit Testing and Code Coverage

• Requirement:
  • Code coverage must be greater than 90%
• Progress:
  • hl7-parser is greater than 80%.
  • data-ingestion-service is greater than 80%.
    • Excluding classes and files.
      • Unused model classes in Jaxb package
        • models in this package are generated after built based on given xml definition
        • Unused model classes
          • AnswerType
          • CaseType
          • ClinicalInformationType
          • CodedType
          • CommonQuestionsType
          • DiseaseSpecificQuestionsType
          • EpidemiologicInformationType
          • HeaderType
          • HierarchicalDesignationType
          • HL7NumericType
          • HL7OBXValueType
          • HL7SNType
          • HL7TMType
          • IdentifiersType
          • IdentifierType
          • InvestigationInformationType
          • LabReportCommmenType
          • LabReportType
          • NameType
          • NoteType
          • NumericType
          • ObjectFactory
          • ObservationsType
          • ObservationType
          • OrganizationParticipantType
          • ParticipantsType
          • PatientType
          • PostalAddressType
          • ProviderNameType
          • ProviderParticipantType
          • ReferenceRangeType
          • ReportingInformationType
          • SectionHeaderType
          • SpecimenType
          • SusceptibilityType
          • TelephoneType
          • TestResultType
          • TestsType
          • UnstructuredType
          • ValuesType
      • Configuration classes
        • DataSourceConfig
        • NbsDataSourceConfig
        • OpenAPIConfig
        • SecurityConfig