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13 Commits

Author SHA1 Message Date
ec2c61b308 Martin's change 2025-05-09 09:23:20 +02:00
0cdd5f371b Use temp directory for secret sync cache 2025-05-09 09:21:40 +02:00
Jan
cd38957dd7 Merge pull request #289 from samply/develop
Merge develop into main
2025-04-15 10:17:11 +02:00
Jan
2ddd535794 feat: ssh tunnel (#292)
* Added ccp module for a ssh tunnel

Usage details under https://github.com/samply/ssh-tunnel

* chore: update ssh-tunnel image to harbor

* feat: ssh tunnel support diffrent port

* chore: fix indentation

* chore: move to top level modules

* docs: add ssh-tunnel docs

---------

Co-authored-by: Tobias Kussel <tobias.kussel@dkfz-heidelberg.de>
2025-04-14 10:45:15 +02:00
Jan
973547c322 chore(transfair): add new gw option (#291) 2025-04-11 08:37:31 +02:00
Jan
6b649c9233 feat: expose transfair via traefik (#290)
Note: Requires a bridgehead install to generate the basic auth user
2025-04-09 13:19:52 +02:00
3144ee5214 Fix GitLab token syncing for BBMRI 2025-03-31 11:08:59 +02:00
68804dc71b feat: add transfair setup to ccp 2025-03-26 13:11:43 +01:00
e5aebfe382 chore!: update transfair config 2025-03-26 13:11:43 +01:00
Jan
4ef585bfc5 Merge pull request #281 from samply/develop
Merge develop into main
2025-03-17 10:02:58 +01:00
6f3aba1eaa feat: support self-signed cert on ttp (#283) 2025-03-12 15:45:55 +01:00
Jan
82ced89b33 chore: unify blaze versioning and upgrade to 0.32 (#277) 2025-03-12 12:52:00 +01:00
6ca67ca082 Merge pull request #270 from samply/develop 2025-02-20 15:46:40 +01:00
24 changed files with 140 additions and 220 deletions

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@ -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"

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@ -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 container_name: bridgehead-cce-blaze
environment: environment:
BASE_URL: "http://bridgehead-cce-blaze:8080" 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' \
--header 'x-api-key: ${EXPORT_API_KEY}'
# QB
curl --location --request POST 'https://${HOST}/cce-reporter/generate?template-id=ccp'

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@ -1,72 +0,0 @@
version: "3.7"
services:
exporter:
image: docker.verbis.dkfz.de/ccp/dktk-exporter:latest
container_name: bridgehead-cce-exporter
environment:
JAVA_OPTS: "-Xms1G -Xmx8G -XX:+UseG1GC"
LOG_LEVEL: "INFO"
EXPORTER_API_KEY: "${EXPORTER_API_KEY}" # Set in exporter-setup.sh
CROSS_ORIGINS: "https://${HOST}"
EXPORTER_DB_USER: "exporter"
EXPORTER_DB_PASSWORD: "${EXPORTER_DB_PASSWORD}" # Set in exporter-setup.sh
EXPORTER_DB_URL: "jdbc:postgresql://exporter-db:5432/exporter"
HTTP_RELATIVE_PATH: "/cce-exporter"
SITE: "${SITE_ID}"
HTTP_SERVLET_REQUEST_SCHEME: "https"
OPAL_PASSWORD: "${EXPORTER_OPAL_PASSWORD}"
labels:
- "traefik.enable=true"
- "traefik.http.routers.exporter_cce.rule=PathPrefix(`/cce-exporter`)"
- "traefik.http.services.exporter_cce.loadbalancer.server.port=8092"
- "traefik.http.routers.exporter_cce.tls=true"
- "traefik.http.middlewares.exporter_cce_strip.stripprefix.prefixes=/cce-exporter"
- "traefik.http.routers.exporter_cce.middlewares=exporter_cce_strip"
volumes:
- "/var/cache/bridgehead/cce/exporter-files:/app/exporter-files/output"
exporter-db:
image: docker.verbis.dkfz.de/cache/postgres:${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}"

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@ -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

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@ -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"
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

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@ -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

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@ -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"

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@ -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"

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@ -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"

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@ -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

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@ -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"

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@ -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"

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@ -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"

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@ -334,24 +334,40 @@ function secret_sync_gitlab_token() {
;; ;;
esac esac
# Use Secret Sync to validate the GitLab token in /var/cache/bridgehead/secrets/gitlab_token. 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/$PROJECT/root.crt.pem"
fi
# Create a temporary directory for Secret Sync that is valid per boot
secret_sync_tempdir="/tmp/bridgehead/secret-sync.boot-$(cat /proc/sys/kernel/random/boot_id)"
mkdir -p $secret_sync_tempdir
# Use Secret Sync to validate the GitLab token in $secret_sync_tempdir/cache.
# If it is missing or expired, Secret Sync will create a new token and write it to the file. # If it is missing or expired, Secret Sync will create a new token and write it to the file.
# The git credential helper reads the token from the file during git pull. # The git credential helper reads the token from the file during git pull.
mkdir -p /var/cache/bridgehead/secrets
touch /var/cache/bridgehead/secrets/gitlab_token # the file has to exist to be mounted correctly in the Docker container
log "INFO" "Running Secret Sync for the GitLab token (gitlab=$gitlab)" log "INFO" "Running Secret Sync for the GitLab token (gitlab=$gitlab)"
docker pull docker.verbis.dkfz.de/cache/samply/secret-sync-local:latest # make sure we have the latest image docker pull docker.verbis.dkfz.de/cache/samply/secret-sync-local:latest # make sure we have the latest image
docker run --rm \ docker run --rm \
-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 \
-v $secret_sync_tempdir:/secret-sync/ \
-e CACHE_PATH=/secret-sync/gitlab-token \
-e TLS_CA_CERTIFICATES_DIR=/conf/trusted-ca-certs \ -e TLS_CA_CERTIFICATES_DIR=/conf/trusted-ca-certs \
-e NO_PROXY=localhost,127.0.0.1 \ -e NO_PROXY=localhost,127.0.0.1 \
-e ALL_PROXY=$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

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@ -2,7 +2,7 @@
[ "$1" = "get" ] || exit [ "$1" = "get" ] || exit
source /var/cache/bridgehead/secrets/gitlab_token source "/tmp/bridgehead/secret-sync.boot-$(cat /proc/sys/kernel/random/boot_id)/gitlab-token"
# Any non-empty username works, only the token matters # Any non-empty username works, only the token matters
cat << EOF cat << EOF

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@ -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 \

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@ -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

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@ -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
View 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!**

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@ -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:

View File

@ -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
} }

View File

@ -1,2 +1,3 @@
FOCUS_TAG=main FOCUS_TAG=main
BEAM_TAG=main BEAM_TAG=main
BLAZE_TAG=0.32

View File

@ -1,2 +1,3 @@
FOCUS_TAG=develop FOCUS_TAG=develop
BEAM_TAG=develop BEAM_TAG=develop
BLAZE_TAG=main