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12 Commits
feature/ad
...
test/obds2
Author | SHA1 | Date | |
---|---|---|---|
d9921568fc | |||
cd38957dd7 | |||
2ddd535794 | |||
973547c322 | |||
6b649c9233 | |||
3144ee5214 | |||
68804dc71b | |||
e5aebfe382 | |||
4ef585bfc5 | |||
6f3aba1eaa | |||
82ced89b33 | |||
6ca67ca082 |
@ -4,7 +4,7 @@ version: "3.7"
|
|||||||
|
|
||||||
services:
|
services:
|
||||||
blaze:
|
blaze:
|
||||||
image: docker.verbis.dkfz.de/cache/samply/blaze:0.31
|
image: docker.verbis.dkfz.de/cache/samply/blaze:${BLAZE_TAG}
|
||||||
container_name: bridgehead-bbmri-blaze
|
container_name: bridgehead-bbmri-blaze
|
||||||
environment:
|
environment:
|
||||||
BASE_URL: "http://bridgehead-bbmri-blaze:8080"
|
BASE_URL: "http://bridgehead-bbmri-blaze:8080"
|
||||||
|
@ -2,7 +2,7 @@ version: "3.7"
|
|||||||
|
|
||||||
services:
|
services:
|
||||||
blaze:
|
blaze:
|
||||||
image: docker.verbis.dkfz.de/cache/samply/blaze:0.31
|
image: docker.verbis.dkfz.de/cache/samply/blaze:${BLAZE_TAG}
|
||||||
container_name: bridgehead-cce-blaze
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container_name: bridgehead-cce-blaze
|
||||||
environment:
|
environment:
|
||||||
BASE_URL: "http://bridgehead-cce-blaze:8080"
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BASE_URL: "http://bridgehead-cce-blaze:8080"
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||||||
|
@ -1,6 +0,0 @@
|
|||||||
# Full Excel Export
|
|
||||||
curl --location --request POST 'https://${HOST}/cce-exporter/request?query=Patient&query-format=FHIR_PATH&template-id=ccp&output-format=EXCEL' \
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|
||||||
--header 'x-api-key: ${EXPORT_API_KEY}'
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|
||||||
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|
||||||
# QB
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||||||
curl --location --request POST 'https://${HOST}/cce-reporter/generate?template-id=ccp'
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|
@ -1,72 +0,0 @@
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|||||||
version: "3.7"
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|
||||||
|
|
||||||
services:
|
|
||||||
exporter:
|
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||||||
image: docker.verbis.dkfz.de/ccp/dktk-exporter:latest
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||||||
container_name: bridgehead-cce-exporter
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||||||
environment:
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|
||||||
JAVA_OPTS: "-Xms1G -Xmx8G -XX:+UseG1GC"
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|
||||||
LOG_LEVEL: "INFO"
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|
||||||
EXPORTER_API_KEY: "${EXPORTER_API_KEY}" # Set in exporter-setup.sh
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|
||||||
CROSS_ORIGINS: "https://${HOST}"
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|
||||||
EXPORTER_DB_USER: "exporter"
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|
||||||
EXPORTER_DB_PASSWORD: "${EXPORTER_DB_PASSWORD}" # Set in exporter-setup.sh
|
|
||||||
EXPORTER_DB_URL: "jdbc:postgresql://exporter-db:5432/exporter"
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|
||||||
HTTP_RELATIVE_PATH: "/cce-exporter"
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|
||||||
SITE: "${SITE_ID}"
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|
||||||
HTTP_SERVLET_REQUEST_SCHEME: "https"
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|
||||||
OPAL_PASSWORD: "${EXPORTER_OPAL_PASSWORD}"
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|
||||||
labels:
|
|
||||||
- "traefik.enable=true"
|
|
||||||
- "traefik.http.routers.exporter_cce.rule=PathPrefix(`/cce-exporter`)"
|
|
||||||
- "traefik.http.services.exporter_cce.loadbalancer.server.port=8092"
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|
||||||
- "traefik.http.routers.exporter_cce.tls=true"
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|
||||||
- "traefik.http.middlewares.exporter_cce_strip.stripprefix.prefixes=/cce-exporter"
|
|
||||||
- "traefik.http.routers.exporter_cce.middlewares=exporter_cce_strip"
|
|
||||||
volumes:
|
|
||||||
- "/var/cache/bridgehead/cce/exporter-files:/app/exporter-files/output"
|
|
||||||
|
|
||||||
exporter-db:
|
|
||||||
image: docker.verbis.dkfz.de/cache/postgres:${POSTGRES_TAG}
|
|
||||||
container_name: bridgehead-cce-exporter-db
|
|
||||||
environment:
|
|
||||||
POSTGRES_USER: "exporter"
|
|
||||||
POSTGRES_PASSWORD: "${EXPORTER_DB_PASSWORD}" # Set in exporter-setup.sh
|
|
||||||
POSTGRES_DB: "exporter"
|
|
||||||
volumes:
|
|
||||||
# Consider removing this volume once we find a solution to save Lens-queries to be executed in the explorer.
|
|
||||||
- "/var/cache/bridgehead/cce/exporter-db:/var/lib/postgresql/data"
|
|
||||||
|
|
||||||
reporter:
|
|
||||||
image: docker.verbis.dkfz.de/ccp/dktk-reporter:latest
|
|
||||||
container_name: bridgehead-cce-reporter
|
|
||||||
environment:
|
|
||||||
JAVA_OPTS: "-Xms1G -Xmx8G -XX:+UseG1GC"
|
|
||||||
LOG_LEVEL: "INFO"
|
|
||||||
CROSS_ORIGINS: "https://${HOST}"
|
|
||||||
HTTP_RELATIVE_PATH: "/cce-reporter"
|
|
||||||
SITE: "${SITE_ID}"
|
|
||||||
EXPORTER_API_KEY: "${EXPORTER_API_KEY}" # Set in exporter-setup.sh
|
|
||||||
EXPORTER_URL: "http://exporter:8092"
|
|
||||||
LOG_FHIR_VALIDATION: "false"
|
|
||||||
HTTP_SERVLET_REQUEST_SCHEME: "https"
|
|
||||||
|
|
||||||
# In this initial development state of the bridgehead, we are trying to have so many volumes as possible.
|
|
||||||
# However, in the first executions in the CCE sites, this volume seems to be very important. A report is
|
|
||||||
# a process that can take several hours, because it depends on the exporter.
|
|
||||||
# There is a risk that the bridgehead restarts, losing the already created export.
|
|
||||||
|
|
||||||
volumes:
|
|
||||||
- "/var/cache/bridgehead/cce/reporter-files:/app/reports"
|
|
||||||
labels:
|
|
||||||
- "traefik.enable=true"
|
|
||||||
- "traefik.http.routers.reporter_cce.rule=PathPrefix(`/cce-reporter`)"
|
|
||||||
- "traefik.http.services.reporter_cce.loadbalancer.server.port=8095"
|
|
||||||
- "traefik.http.routers.reporter_cce.tls=true"
|
|
||||||
- "traefik.http.middlewares.reporter_cce_strip.stripprefix.prefixes=/cce-reporter"
|
|
||||||
- "traefik.http.routers.reporter_cce.middlewares=reporter_cce_strip"
|
|
||||||
|
|
||||||
focus:
|
|
||||||
environment:
|
|
||||||
EXPORTER_URL: "http://exporter:8092"
|
|
||||||
EXPORTER_API_KEY: "${EXPORTER_API_KEY}"
|
|
@ -1,8 +0,0 @@
|
|||||||
#!/bin/bash -e
|
|
||||||
|
|
||||||
if [ "$ENABLE_EXPORTER" == true ]; then
|
|
||||||
log INFO "Exporter setup detected -- will start Exporter service."
|
|
||||||
OVERRIDE+=" -f ./$PROJECT/modules/exporter-compose.yml"
|
|
||||||
EXPORTER_DB_PASSWORD="$(echo \"This is a salt string to generate one consistent password for the exporter. It is not required to be secret.\" | sha1sum | openssl pkeyutl -sign -inkey /etc/bridgehead/pki/${SITE_ID}.priv.pem | base64 | head -c 30)"
|
|
||||||
EXPORTER_API_KEY="$(echo \"This is a salt string to generate one consistent API KEY for the exporter. It is not required to be secret.\" | sha1sum | openssl pkeyutl -sign -inkey /etc/bridgehead/pki/${SITE_ID}.priv.pem | base64 | head -c 64)"
|
|
||||||
fi
|
|
@ -1,89 +0,0 @@
|
|||||||
version: "3.7"
|
|
||||||
|
|
||||||
services:
|
|
||||||
|
|
||||||
teiler-orchestrator:
|
|
||||||
image: docker.verbis.dkfz.de/cache/samply/teiler-orchestrator:latest
|
|
||||||
container_name: bridgehead-teiler-orchestrator
|
|
||||||
labels:
|
|
||||||
- "traefik.enable=true"
|
|
||||||
- "traefik.http.routers.teiler_orchestrator_cce.rule=PathPrefix(`/cce-teiler`)"
|
|
||||||
- "traefik.http.services.teiler_orchestrator_cce.loadbalancer.server.port=9000"
|
|
||||||
- "traefik.http.routers.teiler_orchestrator_cce.tls=true"
|
|
||||||
- "traefik.http.middlewares.teiler_orchestrator_cce_strip.stripprefix.prefixes=/cce-teiler"
|
|
||||||
- "traefik.http.routers.teiler_orchestrator_cce.middlewares=teiler_orchestrator_cce_strip"
|
|
||||||
environment:
|
|
||||||
TEILER_BACKEND_URL: "https://${HOST}/cce-teiler-backend"
|
|
||||||
TEILER_DASHBOARD_URL: "https://${HOST}/cce-teiler-dashboard"
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|
||||||
DEFAULT_LANGUAGE: "${TEILER_DEFAULT_LANGUAGE_LOWER_CASE}"
|
|
||||||
HTTP_RELATIVE_PATH: "/cce-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_cce.rule=PathPrefix(`/cce-teiler-dashboard`)"
|
|
||||||
- "traefik.http.services.teiler_dashboard_cce.loadbalancer.server.port=80"
|
|
||||||
- "traefik.http.routers.teiler_dashboard_cce.tls=true"
|
|
||||||
- "traefik.http.middlewares.teiler_dashboard_cce_strip.stripprefix.prefixes=/cce-teiler-dashboard"
|
|
||||||
- "traefik.http.routers.teiler_dashboard_cce.middlewares=teiler_dashboard_cce_strip"
|
|
||||||
environment:
|
|
||||||
DEFAULT_LANGUAGE: "${TEILER_DEFAULT_LANGUAGE}"
|
|
||||||
TEILER_BACKEND_URL: "https://${HOST}/cce-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}/cce-teiler"
|
|
||||||
TEILER_DASHBOARD_HTTP_RELATIVE_PATH: "/cce-teiler-dashboard"
|
|
||||||
TEILER_ORCHESTRATOR_HTTP_RELATIVE_PATH: "/cce-teiler"
|
|
||||||
TEILER_USER: "${OIDC_USER_GROUP}"
|
|
||||||
TEILER_ADMIN: "${OIDC_ADMIN_GROUP}"
|
|
||||||
REPORTER_DEFAULT_TEMPLATE_ID: "cce-qb"
|
|
||||||
EXPORTER_DEFAULT_TEMPLATE_ID: "cce"
|
|
||||||
|
|
||||||
|
|
||||||
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_cce.rule=PathPrefix(`/cce-teiler-backend`)"
|
|
||||||
- "traefik.http.services.teiler_backend_cce.loadbalancer.server.port=8085"
|
|
||||||
- "traefik.http.routers.teiler_backend_cce.tls=true"
|
|
||||||
- "traefik.http.middlewares.teiler_backend_cce_strip.stripprefix.prefixes=/cce-teiler-backend"
|
|
||||||
- "traefik.http.routers.teiler_backend_cce.middlewares=teiler_backend_cce_strip"
|
|
||||||
environment:
|
|
||||||
LOG_LEVEL: "INFO"
|
|
||||||
APPLICATION_PORT: "8085"
|
|
||||||
APPLICATION_ADDRESS: "${HOST}"
|
|
||||||
DEFAULT_LANGUAGE: "${TEILER_DEFAULT_LANGUAGE}"
|
|
||||||
CONFIG_ENV_VAR_PATH: "/run/secrets/cce.conf"
|
|
||||||
TEILER_ORCHESTRATOR_HTTP_RELATIVE_PATH: "/cce-teiler"
|
|
||||||
TEILER_ORCHESTRATOR_URL: "https://${HOST}/cce-teiler"
|
|
||||||
TEILER_DASHBOARD_DE_URL: "https://${HOST}/cce-teiler-dashboard/de"
|
|
||||||
TEILER_DASHBOARD_EN_URL: "https://${HOST}/cce-teiler-dashboard/en"
|
|
||||||
CENTRAX_URL: "${CENTRAXX_URL}"
|
|
||||||
HTTP_PROXY: "http://forward_proxy:3128"
|
|
||||||
ENABLE_MTBA: "${ENABLE_MTBA}"
|
|
||||||
ENABLE_DATASHIELD: "${ENABLE_DATASHIELD}"
|
|
||||||
TEILER_APP16_BACKENDURL: "https://${HOST}/cce-exporter"
|
|
||||||
TEILER_APP17_BACKENDURL: "https://${HOST}/cce-exporter"
|
|
||||||
TEILER_APP18_BACKENDURL: "https://${HOST}/cce-exporter"
|
|
||||||
TEILER_APP35_BACKENDURL: "https://${HOST}/cce-exporter"
|
|
||||||
TEILER_APP36_BACKENDURL: "https://${HOST}/cce-exporter"
|
|
||||||
TEILER_APP26_BACKENDURL: "https://${HOST}/cce-reporter"
|
|
||||||
|
|
||||||
|
|
||||||
secrets:
|
|
||||||
- cce.conf
|
|
||||||
|
|
||||||
secrets:
|
|
||||||
cce.conf:
|
|
||||||
file: /etc/bridgehead/cce.conf
|
|
@ -1,9 +0,0 @@
|
|||||||
#!/bin/bash -e
|
|
||||||
|
|
||||||
if [ "$ENABLE_TEILER" == true ];then
|
|
||||||
log INFO "Teiler setup detected -- will start Teiler services."
|
|
||||||
OVERRIDE+=" -f ./$PROJECT/modules/teiler-compose.yml"
|
|
||||||
TEILER_DEFAULT_LANGUAGE=DE
|
|
||||||
TEILER_DEFAULT_LANGUAGE_LOWER_CASE=${TEILER_DEFAULT_LANGUAGE,,}
|
|
||||||
add_public_oidc_redirect_url "/cce-teiler/*"
|
|
||||||
fi
|
|
12
cce/vars
12
cce/vars
@ -7,18 +7,6 @@ SUPPORT_EMAIL=manoj.waikar@dkfz-heidelberg.de
|
|||||||
PRIVATEKEYFILENAME=/etc/bridgehead/pki/${SITE_ID}.priv.pem
|
PRIVATEKEYFILENAME=/etc/bridgehead/pki/${SITE_ID}.priv.pem
|
||||||
BROKER_URL_FOR_PREREQ=$BROKER_URL
|
BROKER_URL_FOR_PREREQ=$BROKER_URL
|
||||||
|
|
||||||
POSTGRES_TAG=15.6-alpine
|
|
||||||
|
|
||||||
OIDC_USER_GROUP="CCE_$(capitalize_first_letter ${SITE_ID})"
|
|
||||||
OIDC_ADMIN_GROUP="CCE_$(capitalize_first_letter ${SITE_ID})_Verwalter"
|
|
||||||
OIDC_PRIVATE_CLIENT_ID=${SITE_ID}-private
|
|
||||||
OIDC_PUBLIC_CLIENT_ID=${SITE_ID}-public
|
|
||||||
# Use "test-realm-01" for testing
|
|
||||||
OIDC_REALM="${OIDC_REALM:-test-realm-01}"
|
|
||||||
OIDC_URL="https://login.verbis.dkfz.de"
|
|
||||||
OIDC_ISSUER_URL="${OIDC_URL}/realms/${OIDC_REALM}"
|
|
||||||
OIDC_GROUP_CLAIM="groups"
|
|
||||||
|
|
||||||
for module in $PROJECT/modules/*.sh
|
for module in $PROJECT/modules/*.sh
|
||||||
do
|
do
|
||||||
log DEBUG "sourcing $module"
|
log DEBUG "sourcing $module"
|
||||||
|
@ -2,7 +2,7 @@ version: "3.7"
|
|||||||
|
|
||||||
services:
|
services:
|
||||||
blaze:
|
blaze:
|
||||||
image: docker.verbis.dkfz.de/cache/samply/blaze:0.31
|
image: docker.verbis.dkfz.de/cache/samply/blaze:${BLAZE_TAG}
|
||||||
container_name: bridgehead-ccp-blaze
|
container_name: bridgehead-ccp-blaze
|
||||||
environment:
|
environment:
|
||||||
BASE_URL: "http://bridgehead-ccp-blaze:8080"
|
BASE_URL: "http://bridgehead-ccp-blaze:8080"
|
||||||
|
@ -2,7 +2,7 @@ version: "3.7"
|
|||||||
|
|
||||||
services:
|
services:
|
||||||
blaze-secondary:
|
blaze-secondary:
|
||||||
image: docker.verbis.dkfz.de/cache/samply/blaze:0.31
|
image: docker.verbis.dkfz.de/cache/samply/blaze:${BLAZE_TAG}
|
||||||
container_name: bridgehead-ccp-blaze-secondary
|
container_name: bridgehead-ccp-blaze-secondary
|
||||||
environment:
|
environment:
|
||||||
BASE_URL: "http://bridgehead-ccp-blaze-secondary:8080"
|
BASE_URL: "http://bridgehead-ccp-blaze-secondary:8080"
|
||||||
|
@ -3,7 +3,7 @@ version: "3.7"
|
|||||||
services:
|
services:
|
||||||
obds2fhir-rest:
|
obds2fhir-rest:
|
||||||
container_name: bridgehead-obds2fhir-rest
|
container_name: bridgehead-obds2fhir-rest
|
||||||
image: docker.verbis.dkfz.de/samply/obds2fhir-rest:main
|
image: docker.verbis.dkfz.de/ccp/obds2fhir-rest:fixSampleImport
|
||||||
environment:
|
environment:
|
||||||
IDTYPE: BK_${IDMANAGEMENT_FRIENDLY_ID}_L-ID
|
IDTYPE: BK_${IDMANAGEMENT_FRIENDLY_ID}_L-ID
|
||||||
MAINZELLISTE_APIKEY: ${IDMANAGER_LOCAL_PATIENTLIST_APIKEY}
|
MAINZELLISTE_APIKEY: ${IDMANAGER_LOCAL_PATIENTLIST_APIKEY}
|
||||||
|
10
ccp/vars
10
ccp/vars
@ -29,4 +29,12 @@ done
|
|||||||
idManagementSetup
|
idManagementSetup
|
||||||
mtbaSetup
|
mtbaSetup
|
||||||
obds2fhirRestSetup
|
obds2fhirRestSetup
|
||||||
blazeSecondarySetup
|
blazeSecondarySetup
|
||||||
|
|
||||||
|
for module in modules/*.sh
|
||||||
|
do
|
||||||
|
log DEBUG "sourcing $module"
|
||||||
|
source $module
|
||||||
|
done
|
||||||
|
|
||||||
|
transfairSetup
|
@ -2,7 +2,7 @@ version: "3.7"
|
|||||||
|
|
||||||
services:
|
services:
|
||||||
blaze:
|
blaze:
|
||||||
image: docker.verbis.dkfz.de/cache/samply/blaze:0.31
|
image: docker.verbis.dkfz.de/cache/samply/blaze:${BLAZE_TAG}
|
||||||
container_name: bridgehead-dhki-blaze
|
container_name: bridgehead-dhki-blaze
|
||||||
environment:
|
environment:
|
||||||
BASE_URL: "http://bridgehead-dhki-blaze:8080"
|
BASE_URL: "http://bridgehead-dhki-blaze:8080"
|
||||||
|
@ -2,7 +2,7 @@ version: "3.7"
|
|||||||
|
|
||||||
services:
|
services:
|
||||||
blaze:
|
blaze:
|
||||||
image: docker.verbis.dkfz.de/cache/samply/blaze:0.31
|
image: docker.verbis.dkfz.de/cache/samply/blaze:${BLAZE_TAG}
|
||||||
container_name: bridgehead-itcc-blaze
|
container_name: bridgehead-itcc-blaze
|
||||||
environment:
|
environment:
|
||||||
BASE_URL: "http://bridgehead-itcc-blaze:8080"
|
BASE_URL: "http://bridgehead-itcc-blaze:8080"
|
||||||
|
@ -6,7 +6,7 @@ services:
|
|||||||
replicas: 0 #deactivate landing page
|
replicas: 0 #deactivate landing page
|
||||||
|
|
||||||
blaze:
|
blaze:
|
||||||
image: docker.verbis.dkfz.de/cache/samply/blaze:0.31
|
image: docker.verbis.dkfz.de/cache/samply/blaze:${BLAZE_TAG}
|
||||||
container_name: bridgehead-kr-blaze
|
container_name: bridgehead-kr-blaze
|
||||||
environment:
|
environment:
|
||||||
BASE_URL: "http://bridgehead-kr-blaze:8080"
|
BASE_URL: "http://bridgehead-kr-blaze:8080"
|
||||||
|
@ -334,6 +334,19 @@ function secret_sync_gitlab_token() {
|
|||||||
;;
|
;;
|
||||||
esac
|
esac
|
||||||
|
|
||||||
|
if [ "$PROJECT" == "bbmri" ]; then
|
||||||
|
# If the project is BBMRI, use the BBMRI-ERIC broker and not the GBN broker
|
||||||
|
proxy_id=$ERIC_PROXY_ID
|
||||||
|
broker_url=$ERIC_BROKER_URL
|
||||||
|
broker_id=$ERIC_BROKER_ID
|
||||||
|
root_crt_file="/srv/docker/bridgehead/bbmri/modules/${ERIC_ROOT_CERT}.root.crt.pem"
|
||||||
|
else
|
||||||
|
proxy_id=$PROXY_ID
|
||||||
|
broker_url=$BROKER_URL
|
||||||
|
broker_id=$BROKER_ID
|
||||||
|
root_crt_file="/srv/docker/bridgehead/$PROJECT/root.crt.pem"
|
||||||
|
fi
|
||||||
|
|
||||||
# Use Secret Sync to validate the GitLab token in /var/cache/bridgehead/secrets/gitlab_token.
|
# Use Secret Sync to validate the GitLab token in /var/cache/bridgehead/secrets/gitlab_token.
|
||||||
# If it is missing or expired, Secret Sync will create a new token and write it to the file.
|
# If it is missing or expired, Secret Sync will create a new token and write it to the file.
|
||||||
# The git credential helper reads the token from the file during git pull.
|
# The git credential helper reads the token from the file during git pull.
|
||||||
@ -344,14 +357,14 @@ function secret_sync_gitlab_token() {
|
|||||||
docker run --rm \
|
docker run --rm \
|
||||||
-v /var/cache/bridgehead/secrets/gitlab_token:/usr/local/cache \
|
-v /var/cache/bridgehead/secrets/gitlab_token:/usr/local/cache \
|
||||||
-v $PRIVATEKEYFILENAME:/run/secrets/privkey.pem:ro \
|
-v $PRIVATEKEYFILENAME:/run/secrets/privkey.pem:ro \
|
||||||
-v /srv/docker/bridgehead/$PROJECT/root.crt.pem:/run/secrets/root.crt.pem:ro \
|
-v $root_crt_file:/run/secrets/root.crt.pem:ro \
|
||||||
-v /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro \
|
-v /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro \
|
||||||
-e TLS_CA_CERTIFICATES_DIR=/conf/trusted-ca-certs \
|
-e TLS_CA_CERTIFICATES_DIR=/conf/trusted-ca-certs \
|
||||||
-e NO_PROXY=localhost,127.0.0.1 \
|
-e NO_PROXY=localhost,127.0.0.1 \
|
||||||
-e ALL_PROXY=$HTTPS_PROXY_FULL_URL \
|
-e ALL_PROXY=$HTTPS_PROXY_FULL_URL \
|
||||||
-e PROXY_ID=$PROXY_ID \
|
-e PROXY_ID=$proxy_id \
|
||||||
-e BROKER_URL=$BROKER_URL \
|
-e BROKER_URL=$broker_url \
|
||||||
-e GITLAB_PROJECT_ACCESS_TOKEN_PROVIDER=secret-sync-central.central-secret-sync.$BROKER_ID \
|
-e GITLAB_PROJECT_ACCESS_TOKEN_PROVIDER=secret-sync-central.central-secret-sync.$broker_id \
|
||||||
-e SECRET_DEFINITIONS=GitLabProjectAccessToken:BRIDGEHEAD_CONFIG_REPO_TOKEN:$gitlab \
|
-e SECRET_DEFINITIONS=GitLabProjectAccessToken:BRIDGEHEAD_CONFIG_REPO_TOKEN:$gitlab \
|
||||||
docker.verbis.dkfz.de/cache/samply/secret-sync-local:latest
|
docker.verbis.dkfz.de/cache/samply/secret-sync-local:latest
|
||||||
if [ $? -eq 0 ]; then
|
if [ $? -eq 0 ]; then
|
||||||
|
@ -41,6 +41,14 @@ if [ ! -z "$NNGM_CTS_APIKEY" ] && [ -z "$NNGM_AUTH" ]; then
|
|||||||
add_basic_auth_user "nngm" $generated_passwd "NNGM_AUTH" $PROJECT
|
add_basic_auth_user "nngm" $generated_passwd "NNGM_AUTH" $PROJECT
|
||||||
fi
|
fi
|
||||||
|
|
||||||
|
if [ -z "$TRANSFAIR_AUTH" ]; then
|
||||||
|
if [[ -n "$TTP_URL" || -n "$EXCHANGE_ID_SYSTEM" ]]; then
|
||||||
|
log "INFO" "Now generating basic auth user for transfair API (see adduser in bridgehead for more information). "
|
||||||
|
generated_passwd="$(cat /proc/sys/kernel/random/uuid | sed 's/[-]//g' | head -c 32)"
|
||||||
|
add_basic_auth_user "transfair" $generated_passwd "TRANSFAIR_AUTH" $PROJECT
|
||||||
|
fi
|
||||||
|
fi
|
||||||
|
|
||||||
log "INFO" "Registering system units for bridgehead and bridgehead-update"
|
log "INFO" "Registering system units for bridgehead and bridgehead-update"
|
||||||
cp -v \
|
cp -v \
|
||||||
lib/systemd/bridgehead\@.service \
|
lib/systemd/bridgehead\@.service \
|
||||||
|
17
modules/ssh-tunnel-compose.yml
Normal file
17
modules/ssh-tunnel-compose.yml
Normal file
@ -0,0 +1,17 @@
|
|||||||
|
version: "3.7"
|
||||||
|
|
||||||
|
services:
|
||||||
|
ssh-tunnel:
|
||||||
|
image: docker.verbis.dkfz.de/cache/samply/ssh-tunnel
|
||||||
|
container_name: bridgehead-ccp-ssh-tunnel
|
||||||
|
environment:
|
||||||
|
SSH_TUNNEL_USERNAME: "${SSH_TUNNEL_USERNAME}"
|
||||||
|
SSH_TUNNEL_HOST: "${SSH_TUNNEL_HOST}"
|
||||||
|
SSH_TUNNEL_PORT: "${SSH_TUNNEL_PORT:-22}"
|
||||||
|
volumes:
|
||||||
|
- "/etc/bridgehead/ssh-tunnel.conf:/ssh-tunnel.conf:ro"
|
||||||
|
secrets:
|
||||||
|
- privkey
|
||||||
|
secrets:
|
||||||
|
privkey:
|
||||||
|
file: /etc/bridgehead/pki/ssh-tunnel.priv.pem
|
6
modules/ssh-tunnel-setup.sh
Normal file
6
modules/ssh-tunnel-setup.sh
Normal file
@ -0,0 +1,6 @@
|
|||||||
|
#!/bin/bash
|
||||||
|
|
||||||
|
if [ -n "$ENABLE_SSH_TUNNEL" ]; then
|
||||||
|
log INFO "SSH Tunnel setup detected -- will start SSH Tunnel."
|
||||||
|
OVERRIDE+=" -f ./$PROJECT/modules/ssh-tunnel-compose.yml"
|
||||||
|
fi
|
19
modules/ssh-tunnel.md
Normal file
19
modules/ssh-tunnel.md
Normal file
@ -0,0 +1,19 @@
|
|||||||
|
# SSH Tunnel Module
|
||||||
|
|
||||||
|
This module enables SSH tunneling capabilities for the Bridgehead installation.
|
||||||
|
The primary use case for this is to connect bridgehead components that are hosted externally due to security concerns.
|
||||||
|
To connect the new components to the locally running bridgehead infra one is supposed to write a docker-compose.override.yml changing the urls to point to the corresponding forwarded port of the ssh-tunnel container.
|
||||||
|
|
||||||
|
## Configuration Variables
|
||||||
|
|
||||||
|
- `ENABLE_SSH_TUNNEL`: Required to enable the module
|
||||||
|
- `SSH_TUNNEL_USERNAME`: Username for SSH connection
|
||||||
|
- `SSH_TUNNEL_HOST`: Target host for SSH tunnel
|
||||||
|
- `SSH_TUNNEL_PORT`: SSH port (defaults to 22)
|
||||||
|
|
||||||
|
## Configuration Files
|
||||||
|
|
||||||
|
The module requires the following files to be present:
|
||||||
|
|
||||||
|
- `/etc/bridgehead/ssh-tunnel.conf`: SSH tunnel configuration file. Detailed information can be found [here](https://github.com/samply/ssh-tunnel?tab=readme-ov-file#configuration).
|
||||||
|
- `/etc/bridgehead/pki/ssh-tunnel.priv.pem`: The SSH private key used to connect to the `SSH_TUNNEL_HOST`. **Passphrases for the key are not supported!**
|
@ -5,8 +5,12 @@ services:
|
|||||||
container_name: bridgehead-transfair
|
container_name: bridgehead-transfair
|
||||||
environment:
|
environment:
|
||||||
# NOTE: Those 3 variables need only to be passed if their set, otherwise transfair will complain about empty url values
|
# NOTE: Those 3 variables need only to be passed if their set, otherwise transfair will complain about empty url values
|
||||||
- INSTITUTE_TTP_URL
|
- TTP_URL
|
||||||
- INSTITUTE_TTP_API_KEY
|
- TTP_ML_API_KEY
|
||||||
|
- TTP_GW_SOURCE
|
||||||
|
- TTP_GW_DOMAIN
|
||||||
|
- TTP_TYPE
|
||||||
|
- TTP_AUTH
|
||||||
- PROJECT_ID_SYSTEM
|
- PROJECT_ID_SYSTEM
|
||||||
- FHIR_REQUEST_URL=${FHIR_REQUEST_URL}
|
- FHIR_REQUEST_URL=${FHIR_REQUEST_URL}
|
||||||
- FHIR_INPUT_URL=${FHIR_INPUT_URL}
|
- FHIR_INPUT_URL=${FHIR_INPUT_URL}
|
||||||
@ -17,11 +21,24 @@ services:
|
|||||||
- EXCHANGE_ID_SYSTEM=${EXCHANGE_ID_SYSTEM:-SESSION_ID}
|
- EXCHANGE_ID_SYSTEM=${EXCHANGE_ID_SYSTEM:-SESSION_ID}
|
||||||
- DATABASE_URL=sqlite://transfair/data_requests.sql?mode=rwc
|
- DATABASE_URL=sqlite://transfair/data_requests.sql?mode=rwc
|
||||||
- RUST_LOG=${RUST_LOG:-info}
|
- RUST_LOG=${RUST_LOG:-info}
|
||||||
|
- TLS_CA_CERTIFICATES_DIR=/conf/trusted-ca-certs
|
||||||
volumes:
|
volumes:
|
||||||
- /var/cache/bridgehead/${PROJECT}/transfair:/transfair
|
- /var/cache/bridgehead/${PROJECT}/transfair:/transfair
|
||||||
|
- /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro
|
||||||
|
labels:
|
||||||
|
- "traefik.enable=true"
|
||||||
|
- "traefik.http.middlewares.transfair-strip.stripprefix.prefixes=/transfair"
|
||||||
|
- "traefik.http.routers.transfair.middlewares=transfair-strip,transfair-auth"
|
||||||
|
- "traefik.http.routers.transfair.rule=PathPrefix(`/transfair`)"
|
||||||
|
- "traefik.http.services.transfair.loadbalancer.server.port=8080"
|
||||||
|
- "traefik.http.routers.transfair.tls=true"
|
||||||
|
|
||||||
|
traefik:
|
||||||
|
labels:
|
||||||
|
- "traefik.http.middlewares.transfair-auth.basicauth.users=${TRANSFAIR_AUTH}"
|
||||||
|
|
||||||
transfair-input-blaze:
|
transfair-input-blaze:
|
||||||
image: docker.verbis.dkfz.de/cache/samply/blaze:0.28
|
image: docker.verbis.dkfz.de/cache/samply/blaze:${BLAZE_TAG}
|
||||||
container_name: bridgehead-transfair-input-blaze
|
container_name: bridgehead-transfair-input-blaze
|
||||||
environment:
|
environment:
|
||||||
BASE_URL: "http://bridgehead-transfair-input-blaze:8080"
|
BASE_URL: "http://bridgehead-transfair-input-blaze:8080"
|
||||||
@ -32,9 +49,16 @@ services:
|
|||||||
volumes:
|
volumes:
|
||||||
- "transfair-input-blaze-data:/app/data"
|
- "transfair-input-blaze-data:/app/data"
|
||||||
profiles: ["transfair-input-blaze"]
|
profiles: ["transfair-input-blaze"]
|
||||||
|
labels:
|
||||||
|
- "traefik.enable=true"
|
||||||
|
- "traefik.http.routers.transfair-input-blaze.rule=PathPrefix(`/data-delivery`)"
|
||||||
|
- "traefik.http.middlewares.transfair-input-strip.stripprefix.prefixes=/data-delivery"
|
||||||
|
- "traefik.http.services.transfair-input-blaze.loadbalancer.server.port=8080"
|
||||||
|
- "traefik.http.routers.transfair-input-blaze.middlewares=transfair-input-strip,transfair-auth"
|
||||||
|
- "traefik.http.routers.transfair-input-blaze.tls=true"
|
||||||
|
|
||||||
transfair-request-blaze:
|
transfair-request-blaze:
|
||||||
image: docker.verbis.dkfz.de/cache/samply/blaze:0.28
|
image: docker.verbis.dkfz.de/cache/samply/blaze:${BLAZE_TAG}
|
||||||
container_name: bridgehead-transfair-requests-blaze
|
container_name: bridgehead-transfair-requests-blaze
|
||||||
environment:
|
environment:
|
||||||
BASE_URL: "http://bridgehead-transfair-requests-blaze:8080"
|
BASE_URL: "http://bridgehead-transfair-requests-blaze:8080"
|
||||||
@ -45,6 +69,13 @@ services:
|
|||||||
volumes:
|
volumes:
|
||||||
- "transfair-request-blaze-data:/app/data"
|
- "transfair-request-blaze-data:/app/data"
|
||||||
profiles: ["transfair-request-blaze"]
|
profiles: ["transfair-request-blaze"]
|
||||||
|
labels:
|
||||||
|
- "traefik.enable=true"
|
||||||
|
- "traefik.http.routers.transfair-request-blaze.rule=PathPrefix(`/data-requests`)"
|
||||||
|
- "traefik.http.middlewares.transfair-request-strip.stripprefix.prefixes=/data-requests"
|
||||||
|
- "traefik.http.services.transfair-request-blaze.loadbalancer.server.port=8080"
|
||||||
|
- "traefik.http.routers.transfair-request-blaze.middlewares=transfair-request-strip,transfair-auth"
|
||||||
|
- "traefik.http.routers.transfair-request-blaze.tls=true"
|
||||||
|
|
||||||
volumes:
|
volumes:
|
||||||
transfair-input-blaze-data:
|
transfair-input-blaze-data:
|
||||||
|
@ -1,7 +1,7 @@
|
|||||||
#!/bin/bash -e
|
#!/bin/bash -e
|
||||||
|
|
||||||
function transfairSetup() {
|
function transfairSetup() {
|
||||||
if [[ -n "$INSTITUTE_TTP_URL" || -n "$EXCHANGE_ID_SYSTEM" ]]; then
|
if [[ -n "$TTP_URL" || -n "$EXCHANGE_ID_SYSTEM" ]]; then
|
||||||
echo "Starting transfair."
|
echo "Starting transfair."
|
||||||
OVERRIDE+=" -f ./modules/transfair-compose.yml"
|
OVERRIDE+=" -f ./modules/transfair-compose.yml"
|
||||||
if [ -n "$FHIR_INPUT_URL" ]; then
|
if [ -n "$FHIR_INPUT_URL" ]; then
|
||||||
@ -18,5 +18,14 @@ function transfairSetup() {
|
|||||||
FHIR_REQUEST_URL="http://transfair-requests-blaze:8080"
|
FHIR_REQUEST_URL="http://transfair-requests-blaze:8080"
|
||||||
OVERRIDE+=" --profile transfair-request-blaze"
|
OVERRIDE+=" --profile transfair-request-blaze"
|
||||||
fi
|
fi
|
||||||
|
if [ -n "$TTP_GW_SOURCE" ]; then
|
||||||
|
log INFO "TransFAIR configured with greifswald as ttp"
|
||||||
|
TTP_TYPE="greifswald"
|
||||||
|
elif [ -n "$TTP_ML_API_KEY" ]; then
|
||||||
|
log INFO "TransFAIR configured with mainzelliste as ttp"
|
||||||
|
TTP_TYPE="mainzelliste"
|
||||||
|
else
|
||||||
|
log INFO "TransFAIR configured without ttp"
|
||||||
|
fi
|
||||||
fi
|
fi
|
||||||
}
|
}
|
||||||
|
@ -1,2 +1,3 @@
|
|||||||
FOCUS_TAG=main
|
FOCUS_TAG=main
|
||||||
BEAM_TAG=main
|
BEAM_TAG=main
|
||||||
|
BLAZE_TAG=0.32
|
@ -1,2 +1,3 @@
|
|||||||
FOCUS_TAG=develop
|
FOCUS_TAG=develop
|
||||||
BEAM_TAG=develop
|
BEAM_TAG=develop
|
||||||
|
BLAZE_TAG=main
|
Reference in New Issue
Block a user