bridgehead/bbmri/modules/ehds2-compose.yml

version: "3.7"

services:
  focus-ehds2:
    #image: docker.verbis.dkfz.de/cache/samply/focus:${FOCUS_TAG}
    image: samply/focus
    container_name: bridgehead-focus-ehds2
    environment:
      API_KEY: ${EHDS2_FOCUS_BEAM_SECRET_SHORT}
      BEAM_APP_ID_LONG: focus.${EHDS2_PROXY_ID}
      PROXY_ID: ${EHDS2_PROXY_ID}
      BLAZE_URL: "http://blaze:8080/fhir/"
      BEAM_PROXY_URL: http://beam-proxy-ehds2:8081
      RETRY_COUNT: ${FOCUS_RETRY_COUNT}
      OBFUSCATE: "no"
    depends_on:
      - "beam-proxy-ehds2"
      - "blaze"

  beam-proxy-ehds2:
    image: docker.verbis.dkfz.de/cache/samply/beam-proxy:develop
    container_name: bridgehead-beam-proxy-ehds2
    environment:
      BROKER_URL: ${EHDS2_BROKER_URL}
      PROXY_ID: ${EHDS2_PROXY_ID}
      APP_focus_KEY: ${EHDS2_FOCUS_BEAM_SECRET_SHORT}
      PRIVKEY_FILE: /run/secrets/proxy.pem
      ALL_PROXY: http://forward_proxy:3128
      TLS_CA_CERTIFICATES_DIR: /conf/trusted-ca-certs
      ROOTCERT_FILE: /conf/root.crt.pem
    secrets:
      - proxy.pem
    depends_on:
      - "forward_proxy"
    volumes:
      - /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro
      - /srv/docker/bridgehead/bbmri/modules/${EHDS2_ROOT_CERT}.root.crt.pem:/conf/root.crt.pem:ro

  # Convert ECDC CSV file into FHIR and push to Blaze
  transfair:
    container_name: transfair
    image: samply/transfair
    environment:
      FHIR_INPUT_URL: "http://source_blaze:8080/fhir"
      FHIR_OUTPUT_URL: "http://bridgehead-bbmri-blaze:8080/fhir"
      PROFILE: "amr2fhir"
      #WRITE_BUNDLES_TO_FILE: "true"
      AMR_FILE_PATH: "/app/data"
    restart: on-failure
    # The start up logic for TransFAIR is kind of complicated for the ECDC/EHDS2
    # pilot. This is because we only want to run it if 1. there are source data
    # files to be transformed and 2. if there is no lock file. We also need to
    # wait for Blaze to start, TransFAIR does not check for this. And finally,
    # once TransFAIR has finished loading data, a lock file is created, to stop
    # a time-consuming repeat run.
    command: bash -c " \
             echo listing /app/data && \
             ls -la /app/data && \
             ls /app/data/*.[cC][sS][vV] 1> /dev/null 2>&1 && \
             [ ! -f /app/data/lock ] && \
             ( \
                 echo 'Wait for Blaze to finish initializing' ; \
                 sleep 360 ; \
                 echo 'Remove old output files' ; \
                 rm -rf /app/test/* ; \
                 cd /app ; \
                 echo 'Run TransFAIR' ; \
                 java -jar transFAIR.jar ; \
                 echo 'Touching lock file' ; \
                 touch /app/data/lock \
             ) & tail -f /dev/null"
    # If you put .csv files into ./../ecdc/data, TransFAIR will try to process them.
    volumes:
      - ../../ecdc/test:/app/test/
      - ../../ecdc/data:/app/data/

  # Report on the data pushed to Blaze by TransFAIR
  test-data-loader:
    container_name: test-data-loader
    image: samply/test-data-loader
    command: sh -c "sleep 420 && echo Listing all resources in FHIR store && blazectl --server http://bridgehead-bbmri-blaze:8080/fhir count-resources && tail -f /dev/null"