bridgehead/bbmri/modules/ehds2-compose.yml

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version: "3.7"
services:
focus-ehds2:
image: docker.verbis.dkfz.de/cache/samply/focus:${FOCUS_TAG}
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://blaze:8080/fhir"
PROFILE: "amr2fhir"
AMR_FILE_PATH: "/app/data"
restart: on-failure
command: sh -c "sleep 60 && rm -rf /app/test/* && java -jar transFAIR.jar && tail -f /dev/null"
volumes:
- ./test/:/app/test/
- ./data/:/app/data/
# Report on the data pushed to Blaze by TransFAIR
blazectl:
container_name: blazectl
image: samply/blazectl
command: sh -c "sleep 300 && echo Source store && blazectl --server http://blaze:8080/fhir count-resources && tail -f /dev/null"