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Compare commits
10 Commits
feature/qr
...
feature/op
Author | SHA1 | Date | |
---|---|---|---|
d9208c4be2 | |||
967e45624e | |||
8cd5b93b95 | |||
52c24ee6fa | |||
26712d3567 | |||
eea17c3478 | |||
cf5230963c | |||
23981062bb | |||
8e7fe6851e | |||
760d599b7c |
@ -2,7 +2,7 @@ version: "3.7"
|
|||||||
|
|
||||||
services:
|
services:
|
||||||
focus-eric:
|
focus-eric:
|
||||||
image: docker.verbis.dkfz.de/cache/samply/focus:${FOCUS_TAG}
|
image: docker.verbis.dkfz.de/cache/samply/focus:${FOCUS_TAG}-bbmri
|
||||||
container_name: bridgehead-focus-eric
|
container_name: bridgehead-focus-eric
|
||||||
environment:
|
environment:
|
||||||
API_KEY: ${ERIC_FOCUS_BEAM_SECRET_SHORT}
|
API_KEY: ${ERIC_FOCUS_BEAM_SECRET_SHORT}
|
||||||
|
@ -2,7 +2,7 @@ version: "3.7"
|
|||||||
|
|
||||||
services:
|
services:
|
||||||
focus-gbn:
|
focus-gbn:
|
||||||
image: docker.verbis.dkfz.de/cache/samply/focus:${FOCUS_TAG}
|
image: docker.verbis.dkfz.de/cache/samply/focus:${FOCUS_TAG}-bbmri
|
||||||
container_name: bridgehead-focus-gbn
|
container_name: bridgehead-focus-gbn
|
||||||
environment:
|
environment:
|
||||||
API_KEY: ${GBN_FOCUS_BEAM_SECRET_SHORT}
|
API_KEY: ${GBN_FOCUS_BEAM_SECRET_SHORT}
|
||||||
|
19
bbmri/vars
19
bbmri/vars
@ -1,21 +1,3 @@
|
|||||||
BROKER_ID=broker-test.bbmri-test.samply.de
|
|
||||||
BROKER_URL=https://${BROKER_ID}
|
|
||||||
PROXY_ID=${SITE_ID}.${BROKER_ID}
|
|
||||||
PRIVATEKEYFILENAME=/etc/bridgehead/pki/${SITE_ID}.priv.pem
|
|
||||||
|
|
||||||
BROKER_URL_FOR_PREREQ=$BROKER_URL
|
|
||||||
|
|
||||||
OIDC_USER_GROUP="BBMRI_$(capitalize_first_letter ${SITE_ID})"
|
|
||||||
OIDC_ADMIN_GROUP="BBMRI_$(capitalize_first_letter ${SITE_ID})_Verwalter"
|
|
||||||
OIDC_PUBLIC_CLIENT_ID="BBMRI_${SITE_ID}-public"
|
|
||||||
# Use "test-realm-01" for testing
|
|
||||||
OIDC_REALM="${OIDC_REALM:-test-realm-01}"
|
|
||||||
OIDC_URL="https://login.verbis.dkfz.de"
|
|
||||||
OIDC_ISSUER_URL="${OIDC_URL}/realms/${OIDC_REALM}"
|
|
||||||
OIDC_GROUP_CLAIM="groups"
|
|
||||||
|
|
||||||
POSTGRES_TAG=15.6-alpine
|
|
||||||
|
|
||||||
# Makes sense for all European Biobanks
|
# Makes sense for all European Biobanks
|
||||||
: ${ENABLE_ERIC:=true}
|
: ${ENABLE_ERIC:=true}
|
||||||
|
|
||||||
@ -31,7 +13,6 @@ do
|
|||||||
source $module
|
source $module
|
||||||
done
|
done
|
||||||
|
|
||||||
|
|
||||||
SUPPORT_EMAIL=$ERIC_SUPPORT_EMAIL
|
SUPPORT_EMAIL=$ERIC_SUPPORT_EMAIL
|
||||||
BROKER_URL_FOR_PREREQ="${ERIC_BROKER_URL:-$GBN_BROKER_URL}"
|
BROKER_URL_FOR_PREREQ="${ERIC_BROKER_URL:-$GBN_BROKER_URL}"
|
||||||
|
|
||||||
|
@ -106,8 +106,7 @@ case "$ACTION" in
|
|||||||
loadVars
|
loadVars
|
||||||
hc_send log "Bridgehead $PROJECT startup: Checking requirements ..."
|
hc_send log "Bridgehead $PROJECT startup: Checking requirements ..."
|
||||||
checkRequirements
|
checkRequirements
|
||||||
# NOTE: for testing only, we will need to properly setup secret sync if we want to use this code
|
sync_secrets
|
||||||
# sync_secrets
|
|
||||||
hc_send log "Bridgehead $PROJECT startup: Requirements checked out. Now starting bridgehead ..."
|
hc_send log "Bridgehead $PROJECT startup: Requirements checked out. Now starting bridgehead ..."
|
||||||
exec $COMPOSE -p $PROJECT -f ./minimal/docker-compose.yml -f ./$PROJECT/docker-compose.yml $OVERRIDE up --abort-on-container-exit
|
exec $COMPOSE -p $PROJECT -f ./minimal/docker-compose.yml -f ./$PROJECT/docker-compose.yml $OVERRIDE up --abort-on-container-exit
|
||||||
;;
|
;;
|
||||||
|
@ -22,7 +22,7 @@ services:
|
|||||||
- "traefik.http.routers.blaze_ccp.tls=true"
|
- "traefik.http.routers.blaze_ccp.tls=true"
|
||||||
|
|
||||||
focus:
|
focus:
|
||||||
image: docker.verbis.dkfz.de/cache/samply/focus:${FOCUS_TAG}
|
image: docker.verbis.dkfz.de/cache/samply/focus:${FOCUS_TAG}-dktk
|
||||||
container_name: bridgehead-focus
|
container_name: bridgehead-focus
|
||||||
environment:
|
environment:
|
||||||
API_KEY: ${FOCUS_BEAM_SECRET_SHORT}
|
API_KEY: ${FOCUS_BEAM_SECRET_SHORT}
|
||||||
@ -33,6 +33,7 @@ services:
|
|||||||
RETRY_COUNT: ${FOCUS_RETRY_COUNT}
|
RETRY_COUNT: ${FOCUS_RETRY_COUNT}
|
||||||
EPSILON: 0.28
|
EPSILON: 0.28
|
||||||
QUERIES_TO_CACHE: '/queries_to_cache.conf'
|
QUERIES_TO_CACHE: '/queries_to_cache.conf'
|
||||||
|
ENDPOINT_TYPE: ${FOCUS_ENDPOINT_TYPE:-blaze}
|
||||||
volumes:
|
volumes:
|
||||||
- /srv/docker/bridgehead/ccp/queries_to_cache.conf:/queries_to_cache.conf
|
- /srv/docker/bridgehead/ccp/queries_to_cache.conf:/queries_to_cache.conf
|
||||||
depends_on:
|
depends_on:
|
||||||
@ -58,7 +59,6 @@ services:
|
|||||||
- /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro
|
- /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro
|
||||||
- /srv/docker/bridgehead/ccp/root.crt.pem:/conf/root.crt.pem:ro
|
- /srv/docker/bridgehead/ccp/root.crt.pem:/conf/root.crt.pem:ro
|
||||||
|
|
||||||
|
|
||||||
volumes:
|
volumes:
|
||||||
blaze-data:
|
blaze-data:
|
||||||
|
|
||||||
|
@ -22,7 +22,7 @@ services:
|
|||||||
|
|
||||||
opal:
|
opal:
|
||||||
container_name: bridgehead-opal
|
container_name: bridgehead-opal
|
||||||
image: docker.verbis.dkfz.de/ccp/dktk-opal:latest
|
image: docker.verbis.dkfz.de/ccp/dktk-opal:test
|
||||||
labels:
|
labels:
|
||||||
- "traefik.enable=true"
|
- "traefik.enable=true"
|
||||||
- "traefik.http.routers.opal_ccp.rule=PathPrefix(`/opal`)"
|
- "traefik.http.routers.opal_ccp.rule=PathPrefix(`/opal`)"
|
||||||
|
6
ccp/modules/export-and-qb.curl-templates
Normal file
6
ccp/modules/export-and-qb.curl-templates
Normal file
@ -0,0 +1,6 @@
|
|||||||
|
# Full Excel Export
|
||||||
|
curl --location --request POST 'https://${HOST}/ccp-exporter/request?query=Patient&query-format=FHIR_PATH&template-id=ccp&output-format=EXCEL' \
|
||||||
|
--header 'x-api-key: ${EXPORT_API_KEY}'
|
||||||
|
|
||||||
|
# QB
|
||||||
|
curl --location --request POST 'https://${HOST}/ccp-reporter/generate?template-id=ccp'
|
@ -3,7 +3,7 @@ version: "3.7"
|
|||||||
services:
|
services:
|
||||||
exporter:
|
exporter:
|
||||||
image: docker.verbis.dkfz.de/ccp/dktk-exporter:latest
|
image: docker.verbis.dkfz.de/ccp/dktk-exporter:latest
|
||||||
container_name: bridgehead-${PROJECT}-exporter
|
container_name: bridgehead-ccp-exporter
|
||||||
environment:
|
environment:
|
||||||
JAVA_OPTS: "-Xms1G -Xmx8G -XX:+UseG1GC"
|
JAVA_OPTS: "-Xms1G -Xmx8G -XX:+UseG1GC"
|
||||||
LOG_LEVEL: "INFO"
|
LOG_LEVEL: "INFO"
|
||||||
@ -12,41 +12,39 @@ services:
|
|||||||
EXPORTER_DB_USER: "exporter"
|
EXPORTER_DB_USER: "exporter"
|
||||||
EXPORTER_DB_PASSWORD: "${EXPORTER_DB_PASSWORD}" # Set in exporter-setup.sh
|
EXPORTER_DB_PASSWORD: "${EXPORTER_DB_PASSWORD}" # Set in exporter-setup.sh
|
||||||
EXPORTER_DB_URL: "jdbc:postgresql://exporter-db:5432/exporter"
|
EXPORTER_DB_URL: "jdbc:postgresql://exporter-db:5432/exporter"
|
||||||
HTTP_RELATIVE_PATH: "/${PROJECT}-exporter"
|
HTTP_RELATIVE_PATH: "/ccp-exporter"
|
||||||
SITE: "${SITE_ID}"
|
SITE: "${SITE_ID}"
|
||||||
HTTP_SERVLET_REQUEST_SCHEME: "https"
|
HTTP_SERVLET_REQUEST_SCHEME: "https"
|
||||||
OPAL_PASSWORD: "${EXPORTER_OPAL_PASSWORD}"
|
OPAL_PASSWORD: "${EXPORTER_OPAL_PASSWORD}"
|
||||||
labels:
|
labels:
|
||||||
- "traefik.enable=true"
|
- "traefik.enable=true"
|
||||||
- "traefik.http.routers.exporter_${PROJECT}.rule=PathPrefix(`/${PROJECT}-exporter`)"
|
- "traefik.http.routers.exporter_ccp.rule=PathPrefix(`/ccp-exporter`)"
|
||||||
- "traefik.http.services.exporter_${PROJECT}.loadbalancer.server.port=8092"
|
- "traefik.http.services.exporter_ccp.loadbalancer.server.port=8092"
|
||||||
- "traefik.http.routers.exporter_${PROJECT}.tls=true"
|
- "traefik.http.routers.exporter_ccp.tls=true"
|
||||||
- "traefik.http.middlewares.exporter_${PROJECT}_strip.stripprefix.prefixes=/${PROJECT}-exporter"
|
- "traefik.http.middlewares.exporter_ccp_strip.stripprefix.prefixes=/ccp-exporter"
|
||||||
- "traefik.http.routers.exporter_${PROJECT}.middlewares=exporter_${PROJECT}_strip"
|
- "traefik.http.routers.exporter_ccp.middlewares=exporter_ccp_strip"
|
||||||
- "traefik.http.routers.connector.middlewares=connector_strip,auth-qr"
|
|
||||||
volumes:
|
volumes:
|
||||||
- "/var/cache/bridgehead/${PROJECT}/exporter-files:/app/exporter-files/output"
|
- "/var/cache/bridgehead/ccp/exporter-files:/app/exporter-files/output"
|
||||||
|
|
||||||
|
|
||||||
exporter-db:
|
exporter-db:
|
||||||
image: docker.verbis.dkfz.de/cache/postgres:${POSTGRES_TAG}
|
image: docker.verbis.dkfz.de/cache/postgres:${POSTGRES_TAG}
|
||||||
container_name: bridgehead-${PROJECT}-exporter-db
|
container_name: bridgehead-ccp-exporter-db
|
||||||
environment:
|
environment:
|
||||||
POSTGRES_USER: "exporter"
|
POSTGRES_USER: "exporter"
|
||||||
POSTGRES_PASSWORD: "${EXPORTER_DB_PASSWORD}" # Set in exporter-setup.sh
|
POSTGRES_PASSWORD: "${EXPORTER_DB_PASSWORD}" # Set in exporter-setup.sh
|
||||||
POSTGRES_DB: "exporter"
|
POSTGRES_DB: "exporter"
|
||||||
volumes:
|
volumes:
|
||||||
# Consider removing this volume once we find a solution to save Lens-queries to be executed in the explorer.
|
# Consider removing this volume once we find a solution to save Lens-queries to be executed in the explorer.
|
||||||
- "/var/cache/bridgehead/${PROJECT}/exporter-db:/var/lib/postgresql/data"
|
- "/var/cache/bridgehead/ccp/exporter-db:/var/lib/postgresql/data"
|
||||||
|
|
||||||
reporter:
|
reporter:
|
||||||
image: docker.verbis.dkfz.de/ccp/dktk-reporter:latest
|
image: docker.verbis.dkfz.de/ccp/dktk-reporter:latest
|
||||||
container_name: bridgehead-${PROJECT}-reporter
|
container_name: bridgehead-ccp-reporter
|
||||||
environment:
|
environment:
|
||||||
JAVA_OPTS: "-Xms1G -Xmx8G -XX:+UseG1GC"
|
JAVA_OPTS: "-Xms1G -Xmx8G -XX:+UseG1GC"
|
||||||
LOG_LEVEL: "INFO"
|
LOG_LEVEL: "INFO"
|
||||||
CROSS_ORIGINS: "https://${HOST}"
|
CROSS_ORIGINS: "https://${HOST}"
|
||||||
HTTP_RELATIVE_PATH: "/${PROJECT}-reporter"
|
HTTP_RELATIVE_PATH: "/ccp-reporter"
|
||||||
SITE: "${SITE_ID}"
|
SITE: "${SITE_ID}"
|
||||||
EXPORTER_API_KEY: "${EXPORTER_API_KEY}" # Set in exporter-setup.sh
|
EXPORTER_API_KEY: "${EXPORTER_API_KEY}" # Set in exporter-setup.sh
|
||||||
EXPORTER_URL: "http://exporter:8092"
|
EXPORTER_URL: "http://exporter:8092"
|
||||||
@ -59,15 +57,16 @@ services:
|
|||||||
# There is a risk that the bridgehead restarts, losing the already created export.
|
# There is a risk that the bridgehead restarts, losing the already created export.
|
||||||
|
|
||||||
volumes:
|
volumes:
|
||||||
- "/var/cache/bridgehead/${PROJECT}/reporter-files:/app/reports"
|
- "/var/cache/bridgehead/ccp/reporter-files:/app/reports"
|
||||||
labels:
|
labels:
|
||||||
- "traefik.enable=true"
|
- "traefik.enable=true"
|
||||||
- "traefik.http.routers.reporter_${PROJECT}.rule=PathPrefix(`/${PROJECT}-reporter`)"
|
- "traefik.http.routers.reporter_ccp.rule=PathPrefix(`/ccp-reporter`)"
|
||||||
- "traefik.http.services.reporter_${PROJECT}.loadbalancer.server.port=8095"
|
- "traefik.http.services.reporter_ccp.loadbalancer.server.port=8095"
|
||||||
- "traefik.http.routers.reporter_${PROJECT}.tls=true"
|
- "traefik.http.routers.reporter_ccp.tls=true"
|
||||||
- "traefik.http.middlewares.reporter_${PROJECT}_strip.stripprefix.prefixes=/${PROJECT}-reporter"
|
- "traefik.http.middlewares.reporter_ccp_strip.stripprefix.prefixes=/ccp-reporter"
|
||||||
- "traefik.http.routers.reporter_${PROJECT}.middlewares=reporter_${PROJECT}_strip"
|
- "traefik.http.routers.reporter_ccp.middlewares=reporter_ccp_strip"
|
||||||
|
|
||||||
traefik:
|
focus:
|
||||||
labels:
|
environment:
|
||||||
- "traefik.http.middlewares.auth-qr.basicauth.users=${QR_AUTH}"
|
EXPORTER_URL: "http://exporter:8092"
|
||||||
|
AUTH_HEADER: "${EXPORTER_API_KEY}"
|
@ -23,3 +23,7 @@ services:
|
|||||||
POSTGRES_DB: "dashboard"
|
POSTGRES_DB: "dashboard"
|
||||||
volumes:
|
volumes:
|
||||||
- "/var/cache/bridgehead/ccp/dashboard-db:/var/lib/postgresql/data"
|
- "/var/cache/bridgehead/ccp/dashboard-db:/var/lib/postgresql/data"
|
||||||
|
|
||||||
|
focus:
|
||||||
|
environment:
|
||||||
|
POSTGRES_CONNECTION_STRING: "postgresql://dashboard:${DASHBOARD_DB_PASSWORD}@dashboard-db/dashboard"
|
@ -4,4 +4,5 @@ if [ "$ENABLE_FHIR2SQL" == true ]; then
|
|||||||
log INFO "Dashboard setup detected -- will start Dashboard backend and FHIR2SQL service."
|
log INFO "Dashboard setup detected -- will start Dashboard backend and FHIR2SQL service."
|
||||||
OVERRIDE+=" -f ./$PROJECT/modules/fhir2sql-compose.yml"
|
OVERRIDE+=" -f ./$PROJECT/modules/fhir2sql-compose.yml"
|
||||||
DASHBOARD_DB_PASSWORD="$(generate_simple_password 'fhir2sql')"
|
DASHBOARD_DB_PASSWORD="$(generate_simple_password 'fhir2sql')"
|
||||||
|
FOCUS_ENDPOINT_TYPE="blaze-and-sql"
|
||||||
fi
|
fi
|
||||||
|
@ -101,5 +101,12 @@ services:
|
|||||||
forward_proxy:
|
forward_proxy:
|
||||||
condition: service_healthy
|
condition: service_healthy
|
||||||
|
|
||||||
|
ccp-patient-project-identificator:
|
||||||
|
image: samply/ccp-patient-project-identificator
|
||||||
|
container_name: bridgehead-ccp-patient-project-identificator
|
||||||
|
environment:
|
||||||
|
MAINZELLISTE_APIKEY: ${IDMANAGER_LOCAL_PATIENTLIST_APIKEY}
|
||||||
|
SITE_NAME: ${SITE_NAME}
|
||||||
|
|
||||||
volumes:
|
volumes:
|
||||||
patientlist-db-data:
|
patientlist-db-data:
|
||||||
|
81
ccp/modules/teiler-compose.yml
Normal file
81
ccp/modules/teiler-compose.yml
Normal file
@ -0,0 +1,81 @@
|
|||||||
|
version: "3.7"
|
||||||
|
|
||||||
|
services:
|
||||||
|
|
||||||
|
teiler-orchestrator:
|
||||||
|
image: docker.verbis.dkfz.de/cache/samply/teiler-orchestrator:latest
|
||||||
|
container_name: bridgehead-teiler-orchestrator
|
||||||
|
labels:
|
||||||
|
- "traefik.enable=true"
|
||||||
|
- "traefik.http.routers.teiler_orchestrator_ccp.rule=PathPrefix(`/ccp-teiler`)"
|
||||||
|
- "traefik.http.services.teiler_orchestrator_ccp.loadbalancer.server.port=9000"
|
||||||
|
- "traefik.http.routers.teiler_orchestrator_ccp.tls=true"
|
||||||
|
- "traefik.http.middlewares.teiler_orchestrator_ccp_strip.stripprefix.prefixes=/ccp-teiler"
|
||||||
|
- "traefik.http.routers.teiler_orchestrator_ccp.middlewares=teiler_orchestrator_ccp_strip"
|
||||||
|
environment:
|
||||||
|
TEILER_BACKEND_URL: "https://${HOST}/ccp-teiler-backend"
|
||||||
|
TEILER_DASHBOARD_URL: "https://${HOST}/ccp-teiler-dashboard"
|
||||||
|
DEFAULT_LANGUAGE: "${TEILER_DEFAULT_LANGUAGE_LOWER_CASE}"
|
||||||
|
HTTP_RELATIVE_PATH: "/ccp-teiler"
|
||||||
|
|
||||||
|
teiler-dashboard:
|
||||||
|
image: docker.verbis.dkfz.de/cache/samply/teiler-dashboard:develop
|
||||||
|
container_name: bridgehead-teiler-dashboard
|
||||||
|
labels:
|
||||||
|
- "traefik.enable=true"
|
||||||
|
- "traefik.http.routers.teiler_dashboard_ccp.rule=PathPrefix(`/ccp-teiler-dashboard`)"
|
||||||
|
- "traefik.http.services.teiler_dashboard_ccp.loadbalancer.server.port=80"
|
||||||
|
- "traefik.http.routers.teiler_dashboard_ccp.tls=true"
|
||||||
|
- "traefik.http.middlewares.teiler_dashboard_ccp_strip.stripprefix.prefixes=/ccp-teiler-dashboard"
|
||||||
|
- "traefik.http.routers.teiler_dashboard_ccp.middlewares=teiler_dashboard_ccp_strip"
|
||||||
|
environment:
|
||||||
|
DEFAULT_LANGUAGE: "${TEILER_DEFAULT_LANGUAGE}"
|
||||||
|
TEILER_BACKEND_URL: "https://${HOST}/ccp-teiler-backend"
|
||||||
|
OIDC_URL: "${OIDC_URL}"
|
||||||
|
OIDC_REALM: "${OIDC_REALM}"
|
||||||
|
OIDC_CLIENT_ID: "${OIDC_PUBLIC_CLIENT_ID}"
|
||||||
|
OIDC_TOKEN_GROUP: "${OIDC_GROUP_CLAIM}"
|
||||||
|
TEILER_ADMIN_NAME: "${OPERATOR_FIRST_NAME} ${OPERATOR_LAST_NAME}"
|
||||||
|
TEILER_ADMIN_EMAIL: "${OPERATOR_EMAIL}"
|
||||||
|
TEILER_ADMIN_PHONE: "${OPERATOR_PHONE}"
|
||||||
|
TEILER_PROJECT: "${PROJECT}"
|
||||||
|
EXPORTER_API_KEY: "${EXPORTER_API_KEY}"
|
||||||
|
TEILER_ORCHESTRATOR_URL: "https://${HOST}/ccp-teiler"
|
||||||
|
TEILER_DASHBOARD_HTTP_RELATIVE_PATH: "/ccp-teiler-dashboard"
|
||||||
|
TEILER_ORCHESTRATOR_HTTP_RELATIVE_PATH: "/ccp-teiler"
|
||||||
|
TEILER_USER: "${OIDC_USER_GROUP}"
|
||||||
|
TEILER_ADMIN: "${OIDC_ADMIN_GROUP}"
|
||||||
|
REPORTER_DEFAULT_TEMPLATE_ID: "ccp-qb"
|
||||||
|
EXPORTER_DEFAULT_TEMPLATE_ID: "ccp"
|
||||||
|
|
||||||
|
|
||||||
|
teiler-backend:
|
||||||
|
image: docker.verbis.dkfz.de/ccp/dktk-teiler-backend:latest
|
||||||
|
container_name: bridgehead-teiler-backend
|
||||||
|
labels:
|
||||||
|
- "traefik.enable=true"
|
||||||
|
- "traefik.http.routers.teiler_backend_ccp.rule=PathPrefix(`/ccp-teiler-backend`)"
|
||||||
|
- "traefik.http.services.teiler_backend_ccp.loadbalancer.server.port=8085"
|
||||||
|
- "traefik.http.routers.teiler_backend_ccp.tls=true"
|
||||||
|
- "traefik.http.middlewares.teiler_backend_ccp_strip.stripprefix.prefixes=/ccp-teiler-backend"
|
||||||
|
- "traefik.http.routers.teiler_backend_ccp.middlewares=teiler_backend_ccp_strip"
|
||||||
|
environment:
|
||||||
|
LOG_LEVEL: "INFO"
|
||||||
|
APPLICATION_PORT: "8085"
|
||||||
|
APPLICATION_ADDRESS: "${HOST}"
|
||||||
|
DEFAULT_LANGUAGE: "${TEILER_DEFAULT_LANGUAGE}"
|
||||||
|
CONFIG_ENV_VAR_PATH: "/run/secrets/ccp.conf"
|
||||||
|
TEILER_ORCHESTRATOR_HTTP_RELATIVE_PATH: "/ccp-teiler"
|
||||||
|
TEILER_ORCHESTRATOR_URL: "https://${HOST}/ccp-teiler"
|
||||||
|
TEILER_DASHBOARD_DE_URL: "https://${HOST}/ccp-teiler-dashboard/de"
|
||||||
|
TEILER_DASHBOARD_EN_URL: "https://${HOST}/ccp-teiler-dashboard/en"
|
||||||
|
CENTRAX_URL: "${CENTRAXX_URL}"
|
||||||
|
HTTP_PROXY: "http://forward_proxy:3128"
|
||||||
|
ENABLE_MTBA: "${ENABLE_MTBA}"
|
||||||
|
ENABLE_DATASHIELD: "${ENABLE_DATASHIELD}"
|
||||||
|
secrets:
|
||||||
|
- ccp.conf
|
||||||
|
|
||||||
|
secrets:
|
||||||
|
ccp.conf:
|
||||||
|
file: /etc/bridgehead/ccp.conf
|
@ -5,5 +5,5 @@ if [ "$ENABLE_TEILER" == true ];then
|
|||||||
OVERRIDE+=" -f ./$PROJECT/modules/teiler-compose.yml"
|
OVERRIDE+=" -f ./$PROJECT/modules/teiler-compose.yml"
|
||||||
TEILER_DEFAULT_LANGUAGE=DE
|
TEILER_DEFAULT_LANGUAGE=DE
|
||||||
TEILER_DEFAULT_LANGUAGE_LOWER_CASE=${TEILER_DEFAULT_LANGUAGE,,}
|
TEILER_DEFAULT_LANGUAGE_LOWER_CASE=${TEILER_DEFAULT_LANGUAGE,,}
|
||||||
add_public_oidc_redirect_url "/${PROJECT}-teiler/*"
|
add_public_oidc_redirect_url "/ccp-teiler/*"
|
||||||
fi
|
fi
|
1
ccp/vars
1
ccp/vars
@ -5,7 +5,6 @@ FOCUS_BEAM_SECRET_SHORT="$(cat /proc/sys/kernel/random/uuid | sed 's/[-]//g' | h
|
|||||||
FOCUS_RETRY_COUNT=${FOCUS_RETRY_COUNT:-64}
|
FOCUS_RETRY_COUNT=${FOCUS_RETRY_COUNT:-64}
|
||||||
SUPPORT_EMAIL=support-ccp@dkfz-heidelberg.de
|
SUPPORT_EMAIL=support-ccp@dkfz-heidelberg.de
|
||||||
PRIVATEKEYFILENAME=/etc/bridgehead/pki/${SITE_ID}.priv.pem
|
PRIVATEKEYFILENAME=/etc/bridgehead/pki/${SITE_ID}.priv.pem
|
||||||
PLATFORM=ccp
|
|
||||||
|
|
||||||
BROKER_URL_FOR_PREREQ=$BROKER_URL
|
BROKER_URL_FOR_PREREQ=$BROKER_URL
|
||||||
|
|
||||||
|
@ -35,12 +35,6 @@ if [ -z "$LDM_AUTH" ]; then
|
|||||||
add_basic_auth_user $PROJECT $generated_passwd "LDM_AUTH" $PROJECT
|
add_basic_auth_user $PROJECT $generated_passwd "LDM_AUTH" $PROJECT
|
||||||
fi
|
fi
|
||||||
|
|
||||||
if [ "$ENABLE_EXPORTER" == true ]; then
|
|
||||||
log "INFO" "Now generating basic auth for the quality reports. "
|
|
||||||
generated_passwd="$(cat /proc/sys/kernel/random/uuid | sed 's/[-]//g' | head -c 32)"
|
|
||||||
add_basic_auth_user $PROJECT $generated_passwd "QR_AUTH" $PROJECT
|
|
||||||
fi
|
|
||||||
|
|
||||||
if [ ! -z "$NNGM_CTS_APIKEY" ] && [ -z "$NNGM_AUTH" ]; then
|
if [ ! -z "$NNGM_CTS_APIKEY" ] && [ -z "$NNGM_AUTH" ]; then
|
||||||
log "INFO" "Now generating basic auth for nNGM upload API (see adduser in bridgehead for more information). "
|
log "INFO" "Now generating basic auth for nNGM upload API (see adduser in bridgehead for more information). "
|
||||||
generated_passwd="$(cat /proc/sys/kernel/random/uuid | sed 's/[-]//g' | head -c 32)"
|
generated_passwd="$(cat /proc/sys/kernel/random/uuid | sed 's/[-]//g' | head -c 32)"
|
||||||
|
@ -21,6 +21,7 @@ services:
|
|||||||
- "traefik.http.routers.dashboard.service=api@internal"
|
- "traefik.http.routers.dashboard.service=api@internal"
|
||||||
- "traefik.http.routers.dashboard.tls=true"
|
- "traefik.http.routers.dashboard.tls=true"
|
||||||
- "traefik.http.routers.dashboard.middlewares=auth"
|
- "traefik.http.routers.dashboard.middlewares=auth"
|
||||||
|
- "traefik.http.middlewares.auth.basicauth.users=${LDM_AUTH}"
|
||||||
ports:
|
ports:
|
||||||
- 80:80
|
- 80:80
|
||||||
- 443:443
|
- 443:443
|
||||||
|
@ -1,6 +0,0 @@
|
|||||||
# Full Excel Export
|
|
||||||
curl --location --request POST 'https://${HOST}/${PROJECT}-exporter/request?query=Patient&query-format=FHIR_PATH&template-id=${PROJECT}&output-format=EXCEL' \
|
|
||||||
--header 'x-api-key: ${EXPORT_API_KEY}'
|
|
||||||
|
|
||||||
# QB
|
|
||||||
curl --location --request POST 'https://${HOST}/${PROJECT}-reporter/generate?template-id=${PROJECT}'
|
|
@ -1,82 +0,0 @@
|
|||||||
version: "3.7"
|
|
||||||
|
|
||||||
services:
|
|
||||||
|
|
||||||
teiler-orchestrator:
|
|
||||||
image: docker.verbis.dkfz.de/cache/samply/teiler-orchestrator:latest
|
|
||||||
container_name: bridgehead-teiler-orchestrator
|
|
||||||
labels:
|
|
||||||
- "traefik.enable=true"
|
|
||||||
- "traefik.http.routers.teiler_orchestrator_${PROJECT}.rule=PathPrefix(`/${PROJECT}-teiler`)"
|
|
||||||
- "traefik.http.services.teiler_orchestrator_${PROJECT}.loadbalancer.server.port=9000"
|
|
||||||
- "traefik.http.routers.teiler_orchestrator_${PROJECT}.tls=true"
|
|
||||||
- "traefik.http.middlewares.teiler_orchestrator_${PROJECT}_strip.stripprefix.prefixes=/${PROJECT}-teiler"
|
|
||||||
- "traefik.http.routers.teiler_orchestrator_${PROJECT}.middlewares=teiler_orchestrator_${PROJECT}_strip"
|
|
||||||
environment:
|
|
||||||
TEILER_BACKEND_URL: "https://${HOST}/${PROJECT}-teiler-backend"
|
|
||||||
TEILER_DASHBOARD_URL: "https://${HOST}/${PROJECT}-teiler-dashboard"
|
|
||||||
DEFAULT_LANGUAGE: "${TEILER_DEFAULT_LANGUAGE_LOWER_CASE}"
|
|
||||||
HTTP_RELATIVE_PATH: "/${PROJECT}-teiler"
|
|
||||||
|
|
||||||
teiler-dashboard:
|
|
||||||
#image: docker.verbis.dkfz.de/cache/samply/teiler-dashboard:develop
|
|
||||||
image: docker.verbis.dkfz.de/ccp/samply/teiler-dashboard:bbmri
|
|
||||||
container_name: bridgehead-teiler-dashboard
|
|
||||||
labels:
|
|
||||||
- "traefik.enable=true"
|
|
||||||
- "traefik.http.routers.teiler_dashboard_${PROJECT}.rule=PathPrefix(`/${PROJECT}-teiler-dashboard`)"
|
|
||||||
- "traefik.http.services.teiler_dashboard_${PROJECT}.loadbalancer.server.port=80"
|
|
||||||
- "traefik.http.routers.teiler_dashboard_${PROJECT}.tls=true"
|
|
||||||
- "traefik.http.middlewares.teiler_dashboard_${PROJECT}_strip.stripprefix.prefixes=/${PROJECT}-teiler-dashboard"
|
|
||||||
- "traefik.http.routers.teiler_dashboard_${PROJECT}.middlewares=teiler_dashboard_${PROJECT}_strip"
|
|
||||||
environment:
|
|
||||||
DEFAULT_LANGUAGE: "${TEILER_DEFAULT_LANGUAGE}"
|
|
||||||
TEILER_BACKEND_URL: "https://${HOST}/${PROJECT}-teiler-backend"
|
|
||||||
OIDC_URL: "${OIDC_URL}"
|
|
||||||
OIDC_REALM: "${OIDC_REALM}"
|
|
||||||
OIDC_CLIENT_ID: "${OIDC_PUBLIC_CLIENT_ID}"
|
|
||||||
OIDC_TOKEN_GROUP: "${OIDC_GROUP_CLAIM}"
|
|
||||||
TEILER_ADMIN_NAME: "${OPERATOR_FIRST_NAME} ${OPERATOR_LAST_NAME}"
|
|
||||||
TEILER_ADMIN_EMAIL: "${OPERATOR_EMAIL}"
|
|
||||||
TEILER_ADMIN_PHONE: "${OPERATOR_PHONE}"
|
|
||||||
TEILER_PROJECT: "${PROJECT}"
|
|
||||||
EXPORTER_API_KEY: "${EXPORTER_API_KEY}"
|
|
||||||
TEILER_ORCHESTRATOR_URL: "https://${HOST}/${PROJECT}-teiler"
|
|
||||||
TEILER_DASHBOARD_HTTP_RELATIVE_PATH: "/${PROJECT}-teiler-dashboard"
|
|
||||||
TEILER_ORCHESTRATOR_HTTP_RELATIVE_PATH: "/${PROJECT}-teiler"
|
|
||||||
TEILER_USER: "${OIDC_USER_GROUP}"
|
|
||||||
TEILER_ADMIN: "${OIDC_ADMIN_GROUP}"
|
|
||||||
REPORTER_DEFAULT_TEMPLATE_ID: "${PROJECT}-qb"
|
|
||||||
EXPORTER_DEFAULT_TEMPLATE_ID: "${PROJECT}"
|
|
||||||
|
|
||||||
|
|
||||||
teiler-backend:
|
|
||||||
image: docker.verbis.dkfz.de/ccp/${PROJECT}-teiler-backend:latest
|
|
||||||
container_name: bridgehead-teiler-backend
|
|
||||||
labels:
|
|
||||||
- "traefik.enable=true"
|
|
||||||
- "traefik.http.routers.teiler_backend_${PROJECT}.rule=PathPrefix(`/${PROJECT}-teiler-backend`)"
|
|
||||||
- "traefik.http.services.teiler_backend_${PROJECT}.loadbalancer.server.port=8085"
|
|
||||||
- "traefik.http.routers.teiler_backend_${PROJECT}.tls=true"
|
|
||||||
- "traefik.http.middlewares.teiler_backend_${PROJECT}_strip.stripprefix.prefixes=/${PROJECT}-teiler-backend"
|
|
||||||
- "traefik.http.routers.teiler_backend_${PROJECT}.middlewares=teiler_backend_${PROJECT}_strip"
|
|
||||||
environment:
|
|
||||||
LOG_LEVEL: "INFO"
|
|
||||||
APPLICATION_PORT: "8085"
|
|
||||||
APPLICATION_ADDRESS: "${HOST}"
|
|
||||||
DEFAULT_LANGUAGE: "${TEILER_DEFAULT_LANGUAGE}"
|
|
||||||
CONFIG_ENV_VAR_PATH: "/run/secrets/project-conf"
|
|
||||||
TEILER_ORCHESTRATOR_HTTP_RELATIVE_PATH: "/${PROJECT}-teiler"
|
|
||||||
TEILER_ORCHESTRATOR_URL: "https://${HOST}/${PROJECT}-teiler"
|
|
||||||
TEILER_DASHBOARD_DE_URL: "https://${HOST}/${PROJECT}-teiler-dashboard/de"
|
|
||||||
TEILER_DASHBOARD_EN_URL: "https://${HOST}/${PROJECT}-teiler-dashboard/en"
|
|
||||||
CENTRAX_URL: "${CENTRAXX_URL}"
|
|
||||||
HTTP_PROXY: "http://forward_proxy:3128"
|
|
||||||
ENABLE_MTBA: "${ENABLE_MTBA}"
|
|
||||||
ENABLE_DATASHIELD: "${ENABLE_DATASHIELD}"
|
|
||||||
secrets:
|
|
||||||
- project-conf
|
|
||||||
|
|
||||||
secrets:
|
|
||||||
project-conf:
|
|
||||||
file: "/etc/bridgehead/${PROJECT}.conf"
|
|
Reference in New Issue
Block a user