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Development environment setup

Following this guide will set up a fully functioning local development environment. You will be able to ingest and process Electronic Lab Reports (ELRs), debug the various services, and view the processed patient data within NBS 6.

Building

  1. Provide the necessary configurations
  2. Optional: Build and deploy NBS 6 Wildfly docker container 
    ./containers/build_classic.sh
  3. Start Keycloak, Kafka, and database container 
    docker compose up di-keycloak broker zookeeper di-mssql -d
  4. Start data-ingestion-service with gradle. Allows remote debugging using port 19040 
    ./gradlew data-ingestion-service:bootRun
  5. Start data-processing-service with gradle. Allows remote debugging using port 19041 
    ./gradlew data-processing-service:bootRun
  6. Optional: Start Record Linkage service 
    docker compose up di-record-linker -d
  7. Optional: Start deduplication service with gradle. Allows remote debugging using port 19042 (Note: Sync and Record Linker communcation are feature flagged off by default) 
    ./gradlew deduplication:bootRun

Once the above steps have been completed, the postman collection can be used to fetch an authentication token from Keycloak, submit an ELR, and check the status of the ELR.

Swagger pages are also available

  1. data-ingestion-service
  2. data-processing-service
  3. deduplication

If the optional NBS 6 WildFly container was built, NBS 6 can be accessed here.

Configuration

The docker compose file supports pulling information from a .dataingestion.env file and each service supports creating an application-local.yml. Below are sample configuration files.

dataingestion.env - place at the project root, alongside the docker-compose.yml

DI_AUTH_URI=http://di-keycloak:8080/realms/NBS
RTI_CACHE_AUTH_URI=http://di-keycloak:8080/realms/NBS

NBS_DBSERVER=di-mssql:1433
NBS_DBUSER=sa
NBS_DBPASSWORD=fake.fake.fake.1234
KC_BOOTSTRAP_ADMIN_USERNAME=admin
KC_BOOTSTRAP_ADMIN_PASSWORD=fake.fake.fake.1234

DB_URI=mssql+pyodbc://sa:fake.fake.fake.1234@di-mssql:1433/mpi?driver=ODBC+Driver+18+for+SQL+Server&TrustServerCertificate=yes

data-ingestion-service/src/main/resources/application-local.yaml

spring:
  security:
    oauth2:
      resourceserver:
        jwt:
          issuer-uri: http://localhost:8101/realms/NBS
  datasource:
    username: sa
    password: fake.fake.fake.1234
    dataingest:
      url: jdbc:sqlserver://localhost:2433;databaseName=NBS_DATAINGEST;encrypt=true;trustServerCertificate=true;
    msgoute:
      url: jdbc:sqlserver://localhost:2433;databaseName=NBS_MSGOUTE;encrypt=true;trustServerCertificate=true;
    odse:
      url: jdbc:sqlserver://localhost:2433;databaseName=NBS_ODSE;encrypt=true;trustServerCertificate=true;

data-processing-service/src/main/resources/application-local.yaml

spring:
  datasource:
    username: sa
    password: fake.fake.fake.1234
    nbs:
      url: jdbc:sqlserver://localhost:2433;databaseName=NBS_MSGOUTE;encrypt=true;trustServerCertificate=true;
    odse:
      url: jdbc:sqlserver://localhost:2433;databaseName=NBS_ODSE;encrypt=true;trustServerCertificate=true;
    srte:
      url: jdbc:sqlserver://localhost:2433;databaseName=NBS_SRTE;encrypt=true;trustServerCertificate=true;

features:
  modernizedMatching:
    enabled: true
    url: http://localhost:8083/api/deduplication/

deduplication/src/main/resources/application-local.yaml

spring:
  datasource:
    deduplication:
      url: jdbc:sqlserver://localhost:2433;database=deduplication;encrypt=true;trustServerCertificate=true;
      username: sa
      password: fake.fake.fake.1234
    nbs:
      url: jdbc:sqlserver://localhost:2433;database=nbs_odse;encrypt=true;trustServerCertificate=true;
      username: sa
      password: fake.fake.fake.1234
    mpi:
      url: jdbc:postgresql://localhost:5432/postgres
      username: postgres
      password: pw
  batch:
    jdbc:
      initialize-schema: always

logging:
  level:
    org.springframework.jdbc.core.JdbcTemplate: debug

Remote debugging in VS Code

The data-ingestion-service and data-processing-service have been configured to allow remote debugging when started through ./gradlew <service-name>:bootRun. The following launch.json will enable VS-Code to connect to these services for debugging.

{
  "version": "0.2.0",
  "configurations": [
    {
      "type": "java",
      "name": "Data Ingestion (Attach)",
      "projectName": "data-ingestion-service",
      "request": "attach",
      "hostName": "localhost",
      "port": 19040
    },
    {
      "type": "java",
      "name": "Data Processing (Attach)",
      "projectName": "data-processing-service",
      "request": "attach",
      "hostName": "localhost",
      "port": 19041
    },
    {
      "type": "java",
      "name": "Deduplication (Attach)",
      "projectName": "Modernization-API",
      "request": "attach",
      "hostName": "localhost",
      "port": 19042
    }
  ]
}