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}
    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
    #command: sh -c "sleep 60 && rm -rf /app/test/* && ([ ! -f "/app/lock" && ] && java -jar transFAIR.jar && touch "/app/lock) && tail -f /dev/null"
    #command: sh -c "sleep 60 && rm -rf /app/test/* && java -jar transFAIR.jar && tail -f /dev/null"
    #command: sh -c "echo listing /app/data && ls -la /app/data && /app/launch.sh"
    #command: sh -c "echo listing /app/data && ls -la /app/data && [ "$(ls -A /app/data)" ] && [ ! -f "/app/data/lock" ] && /app/launch.sh & tail -f /dev/null"
    #command: sh -c "echo listing /app/data && ls -la /app/data && [ ! -z "$(ls -A /app/data)" ] && [ ! -f "/app/data/lock" ] && /app/launch.sh & tail -f /dev/null"
    #command: bash -c "echo listing /app/data && ls -la /app/data && [ ! -z "$(ls -A /app/data)" ] && [ ! -f "/app/data/lock" ] && /app/launch.sh & tail -f /dev/null"
    #command: bash -c "echo listing /app/data && ls -la /app/data && [ ! -f "/app/data/lock" ] && /app/launch.sh & tail -f /dev/null"
    #command: bash -c "echo listing /app/data && ls -la /app/data && [ ! -z "$(find /app/data -mindepth 1 -maxdepth 1)" ] && [ ! -f "/app/data/lock" ] && /app/launch.sh & tail -f /dev/null"
    #command: bash -c "echo listing /app/data && ls -la /app/data && [ ! -z $(ls -A /app/data) ] && [ ! -f /app/data/lock ] && /app/launch.sh & tail -f /dev/null"
    #command: bash -c "echo listing /app/data && ls -la /app/data && [ ! -f /app/data/lock ] && /app/launch.sh & tail -f /dev/null" # works!
    #command: bash -c "echo listing /app/data && ls -la /app/data && [ ! -z `ls -A /app/data` ] && [ ! -f /app/data/lock ] && /app/launch.sh & tail -f /dev/null"
    #command: bash -c "echo listing /app/data && ls -la /app/data && [ -f /app/data/*.csv ] && [ ! -f /app/data/lock ] && /app/launch.sh & tail -f /dev/null" # works!
    command: bash -c "echo listing /app/data && ls -la /app/data && [ -f /app/data/*.[cC][sS][vV] ] && [ ! -f /app/data/lock ] && /app/launch.sh & tail -f /dev/null"
    #command: sh -c "echo listing /app/data && ls -la /app/data && [ ! -z $(ls -A /app/data) ] && [ ! -f /app/data/lock ] && /app/launch.sh & tail -f /dev/null"
    #command: sh -c "rm -rf /app/test/* && java -jar transFAIR.jar"
    volumes:
      #- /home/gerhard/Projects/EHDS2/PrototypeSpring2024/test/:/app/test/
      #- /home/gerhard/Projects/EHDS2/PrototypeSpring2024/Data/:/app/data/
      #- ../ecdc/test:/app/test/
      #- ../ecdc/data:/app/data/
      - ../../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 300 && echo Listing all resources in FHIR store && blazectl --server http://bridgehead-bbmri-blaze:8080/fhir count-resources && tail -f /dev/null"