add beamsel to onkofdz docker compose

This commit is contained in:
Tobias Kussel 2024-09-11 19:58:54 +00:00
parent 82b09bd452
commit 92a6b60acb
2 changed files with 76 additions and 12 deletions

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@ -11,6 +11,7 @@ services:
ALL_PROXY: http://forward_proxy:3128 ALL_PROXY: http://forward_proxy:3128
TLS_CA_CERTIFICATES_DIR: /conf/trusted-ca-certs TLS_CA_CERTIFICATES_DIR: /conf/trusted-ca-certs
ROOTCERT_FILE: /conf/root.crt.pem ROOTCERT_FILE: /conf/root.crt.pem
app_beamsel_key: ${BEAMSEL_SECRET}
secrets: secrets:
- proxy.pem - proxy.pem
depends_on: depends_on:
@ -18,7 +19,69 @@ services:
volumes: volumes:
- /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro - /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro
- /srv/docker/bridgehead/minimal/modules/onko.root.crt.pem:/conf/root.crt.pem: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: secrets:
proxy.pem: proxy.pem:
file: /etc/bridgehead/pki/${SITE_ID}.priv.pem file: /etc/bridgehead/pki/${SITE_ID}.priv.pem

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@ -1,14 +1,15 @@
#!/bin/bash #!/bin/bash
BROKER_ID=test-no-real-data.broker.samply.de if [ -n "${ENABLE_ONKOFDZ}" ]; then
BROKER_URL=https://${BROKER_ID} BROKER_ID=test-no-real-data.broker.samply.de
PROXY_ID=${SITE_ID}.${BROKER_ID} BROKER_URL=https://${BROKER_ID}
FOCUS_BEAM_SECRET_SHORT="$(cat /proc/sys/kernel/random/uuid | sed 's/[-]//g' | head -c 20)" PROXY_ID=${SITE_ID}.${BROKER_ID}
FOCUS_RETRY_COUNT=${FOCUS_RETRY_COUNT:-64} BEAMSEL_SECRET="$(cat /proc/sys/kernel/random/uuid | sed 's/[-]//g' | head -c 20)"
SUPPORT_EMAIL=support-ccp@dkfz-heidelberg.de SUPPORT_EMAIL=support-ccp@dkfz-heidelberg.de
PRIVATEKEYFILENAME=/etc/bridgehead/pki/${SITE_ID}.priv.pem PRIVATEKEYFILENAME=/etc/bridgehead/pki/${SITE_ID}.priv.pem
BROKER_URL_FOR_PREREQ=$BROKER_URL BROKER_URL_FOR_PREREQ=$BROKER_URL
log INFO "Loading OnkoFDZ module" log INFO "Loading OnkoFDZ module"
OVERRIDE+=" -f ./$PROJECT/modules/onkofdz-compose.yml" OVERRIDE+=" -f ./$PROJECT/modules/onkofdz-compose.yml"
fi