diff --git a/minimal/modules/onkofdz-compose.yml b/minimal/modules/onkofdz-compose.yml index e6b0171..c8db300 100644 --- a/minimal/modules/onkofdz-compose.yml +++ b/minimal/modules/onkofdz-compose.yml @@ -11,6 +11,7 @@ services: ALL_PROXY: http://forward_proxy:3128 TLS_CA_CERTIFICATES_DIR: /conf/trusted-ca-certs ROOTCERT_FILE: /conf/root.crt.pem + app_beamsel_key: ${BEAMSEL_SECRET} secrets: - proxy.pem depends_on: @@ -18,7 +19,69 @@ services: volumes: - /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro - /srv/docker/bridgehead/minimal/modules/onko.root.crt.pem:/conf/root.crt.pem:ro - + postgres: + image: postgres:9.5-alpine + environment: + POSTGRES_DB: mainzelliste-sel + POSTGRES_USER: mainzelliste-sel + POSTGRES_PASSWORD: ${MAINZELLISTE_DB_PASSWORD} + volumes: + # - ./postgres-logs:/var/log/postgresql + - ml-data:/var/lib/postgresql/data + depends_on: + - secureepilinker + mainzelliste: + image: medicalinformatics/mainzelliste:secureepilinker-alpha + environment: + ML_API_KEY: ${LOCAL_SEL_API_KEY} + ML_DB_HOST: postgres + ML_DB_PORT: 5432 + ML_DB_USER: mainzelliste-sel + ML_DB_NAME: mainzelliste-sel + ML_DB_PASS: ${MAINZELLISTE_DB_PASSWORD} + ML_LOCAL_ID: ${SITE_ID} + ML_LOCAL_SEL_URL: http://secureepilinker:8161 + ML_LOCAL_CALLBACK_LINK_URL: http://mainzelliste:8080/Communicator/linkCallback + ML_LOCAL_CALLBACK_MATCH_URL: http://mainzelliste:8080/Communicator/matchCallback/${REMOTE_SEL_SITE} + ML_LOCAL_DATA_SERVICE_URL: http://mainzelliste:8080/Communicator/getAllRecords + ML_LOCAL_AUTHENTICATION_TYPE: apiKey + ML_LOCAL_API_KEY: ${LOCAL_SEL_API_KEY} + ML_SERVER_0_REMOTEID: ${REMOTE_SEL_SITE} + ML_SERVER_0_IDTYPE: link-${SITE_ID}-${REMOTE_SEL_SITE} + ML_SERVER_0_REMOTE_SEL_URL: http://beamsel:8080 + ML_SERVER_0_APIKEY: ${REMOTE_SEL_API_KEY} + ### Linkage Service not used for matching + ML_SERVER_0_LINKAGE_SERVICE_BASE_URL: ${LS_SEL_URL} + ML_SERVER_0_LINKAGE_SERVICE_AUTH_TYPE: apiKey + ML_SERVER_0_LINKAGE_SERVICE_SHARED_KEY: ${LS_SEL_SHARED_KEY} + ML_LOG_MODE: stdout #stdout=stdout everything else =logging in mainzelliste.log + ML_LOG_LEVEL: INFO + no_proxy: "localhost,secureepilinker" + volumes: + # - ./logs:/usr/local/tomcat/logs/ + - /etc/bridgehead/onkofdz/config/mainzelliste.conf.docker:/run/secrets/mainzelliste.docker.conf + - /etc/bridgehead/onkofdz/config/sel.conf.docker:/run/secrets/sel.docker.conf + depends_on: + - postgres + - secureepilinker + secureepilinker: + image: docker.verbis.dkfz.de/onkofdz/secureepilinker:beamsel + environment: + no_proxy: "mainzelliste,beamsel" + volumes: + - "/etc/bridgehead/onkofdz/config/epilinker.serverconf.json:/data/serverconf.json" + command: '-vvvv' + beamsel: + image: docker.verbis.dkfz.de/onkofdz/beam-sel + environment: + BEAM_URL: "http://beam-proxy:8081" + BEAM_SECRET: ${BEAMSEL_SECRET} + BEAM_ID: beamsel.${PROXY_ID} + SEL_ADDR: "secureepilinker:8161" + depends_on: + - secureepilinker +volumes: + ml-data: secrets: proxy.pem: - file: /etc/bridgehead/pki/${SITE_ID}.priv.pem \ No newline at end of file + file: /etc/bridgehead/pki/${SITE_ID}.priv.pem diff --git a/minimal/modules/onkofdz-setup.sh b/minimal/modules/onkofdz-setup.sh index 58ad789..4fcb1e4 100644 --- a/minimal/modules/onkofdz-setup.sh +++ b/minimal/modules/onkofdz-setup.sh @@ -1,14 +1,15 @@ #!/bin/bash -BROKER_ID=test-no-real-data.broker.samply.de -BROKER_URL=https://${BROKER_ID} -PROXY_ID=${SITE_ID}.${BROKER_ID} -FOCUS_BEAM_SECRET_SHORT="$(cat /proc/sys/kernel/random/uuid | sed 's/[-]//g' | head -c 20)" -FOCUS_RETRY_COUNT=${FOCUS_RETRY_COUNT:-64} -SUPPORT_EMAIL=support-ccp@dkfz-heidelberg.de -PRIVATEKEYFILENAME=/etc/bridgehead/pki/${SITE_ID}.priv.pem +if [ -n "${ENABLE_ONKOFDZ}" ]; then + BROKER_ID=test-no-real-data.broker.samply.de + BROKER_URL=https://${BROKER_ID} + PROXY_ID=${SITE_ID}.${BROKER_ID} + BEAMSEL_SECRET="$(cat /proc/sys/kernel/random/uuid | sed 's/[-]//g' | head -c 20)" + SUPPORT_EMAIL=support-ccp@dkfz-heidelberg.de + PRIVATEKEYFILENAME=/etc/bridgehead/pki/${SITE_ID}.priv.pem -BROKER_URL_FOR_PREREQ=$BROKER_URL + BROKER_URL_FOR_PREREQ=$BROKER_URL -log INFO "Loading OnkoFDZ module" -OVERRIDE+=" -f ./$PROJECT/modules/onkofdz-compose.yml" \ No newline at end of file + log INFO "Loading OnkoFDZ module" + OVERRIDE+=" -f ./$PROJECT/modules/onkofdz-compose.yml" +fi