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37 Commits

Author SHA1 Message Date
ae80e6bb9d Bugfix: teiler backend secret 2025-05-23 18:09:08 +02:00
6476529abd Teiler in BBMRI 2025-05-22 14:30:30 +02:00
af08a9fb08 chore: change some teiler variables (#307) 2025-05-20 16:24:24 +02:00
b95f0efbe7 fix: add own url to teiler dashboard to make it offline compatible (#305) 2025-05-20 09:39:14 +02:00
99567e2b40 fix: Ensure transfair can properly communicate with the fhir server for requests (#304) 2025-05-19 17:01:37 +02:00
Jan
96ff6043a1 feat: allow transfair to talk to services behind the proxy (#296) 2025-05-09 13:52:33 +02:00
Jan
844ce3386e chore(transfair): update transfair config (#298) 2025-05-09 11:30:26 +02:00
9782bf66b6 Code review: Move to /tmp/bridgehead/... 2025-05-08 09:18:02 +02:00
87f0e8ad7f Use temp directory for secret sync cache 2025-05-08 09:18:02 +02:00
Jan
7365be3e7b chore(transfair): add option to disable tls verification (#295) 2025-04-17 12:01:45 +02:00
c5d08c50a4 chore: add BBMRI ERIC acceptance env (#294) 2025-04-16 15:37:55 +02:00
Jan
72ecaadba8 fix: ssh-tunnel-setup.sh (#293) 2025-04-15 11:36:20 +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
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
5d94bac0e2 Mount queries_to_cache.conf readonly (#282) 2025-03-10 16:03:05 +01:00
83555540f5 chore: update central Secret Sync proxy ID (#280) 2025-03-10 12:08:19 +01:00
e396e00178 Fix/ccp cql cache (#279)
* fix: adapt focus caching to new cql and add focus caching for cce and itcc

---------

Co-authored-by: p.delpy@dkfz-heidelberg.de <p.delpy@dkfz-heidelberg.de>
2025-03-07 12:20:38 +01:00
ecb29830e4 Send the origin of /etc/bridgehead repo to Secret Sync
This is to anticipate an upcoming change in Secret Sync that will allow it to support multiple GitLab servers, e.g. verbis GitLab and BBMRI GitLab.
2025-03-05 11:04:22 +01:00
98121c17e8 Make Codeowners Rule apply to all Files in Repo 2025-02-20 17:28:38 +01:00
e38511e118 Add Codeowners File 2025-02-20 17:20:54 +01:00
8334fac84d fix: use correct obds2fhir-rest image
---------

Co-authored-by: Pierre Delpy <p.delpy@dkfz-heidelberg.de>
2025-02-20 13:48:10 +01:00
8000356b57 docs: explicitly clone main branch (#269) 2025-02-07 11:21:43 +01:00
74d8e68d96 Merge pull request #258 from samply/feat/routine-connector
feat: transFAIR
2025-02-07 10:39:54 +01:00
c568a56651 refactor: set transfair log to info 2025-02-07 10:30:43 +01:00
8384143387 fix: make transfair reach the internal blaze stores 2025-02-07 09:17:17 +01:00
8fe73a8123 fix: support mode without ttp 2025-02-07 09:17:07 +01:00
bca63e82a9 fix: don't use return in transfairSetup
For some reason the return not only exits transfairSetup, but also the
bridgehead script
2025-02-06 15:43:37 +01:00
fa0d9fb8b4 restrict additional blaze memory usage 2025-01-24 09:23:08 +00:00
139fcecabe redo transfair setup 2025-01-23 13:27:42 +00:00
2058a7a5c9 update image url 2025-01-23 12:06:43 +00:00
47364f999e wip: routine connector 2025-01-21 13:55:08 +00:00
37 changed files with 418 additions and 125 deletions

1
.github/CODEOWNERS vendored Normal file
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@ -0,0 +1 @@
* @samply/bridgehead-developers

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@ -154,7 +154,7 @@ Pay special attention to:
Clone the bridgehead repository:
```shell
sudo mkdir -p /srv/docker/
sudo git clone https://github.com/samply/bridgehead.git /srv/docker/bridgehead
sudo git clone -b main https://github.com/samply/bridgehead.git /srv/docker/bridgehead
```
Then, run the installation script:

View File

@ -4,7 +4,7 @@ version: "3.7"
services:
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
environment:
BASE_URL: "http://bridgehead-bbmri-blaze:8080"

View File

@ -10,6 +10,10 @@ if [ "${ENABLE_ERIC}" == "true" ]; then
export ERIC_BROKER_ID=broker.bbmri.samply.de
export ERIC_ROOT_CERT=eric
;;
"acceptance")
export ERIC_BROKER_ID=broker-acc.bbmri-acc.samply.de
export ERIC_ROOT_CERT=eric.acc
;;
"test")
export ERIC_BROKER_ID=broker-test.bbmri-test.samply.de
export ERIC_ROOT_CERT=eric.test

View File

@ -0,0 +1,20 @@
-----BEGIN CERTIFICATE-----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-----END CERTIFICATE-----

View File

@ -1,3 +1,25 @@
DEFAULT_LANGUAGE=EN
DEFAULT_LANGUAGE_LOWER_CASE=${DEFAULT_LANGUAGE,,}
BROKER_ID=broker-test.bbmri-test.samply.de
BROKER_URL=https://${BROKER_ID}
PROXY_ID=${SITE_ID}.${BROKER_ID}
PRIVATEKEYFILENAME=/etc/bridgehead/pki/${SITE_ID}.priv.pem
PLATFORM=bbmri
BROKER_URL_FOR_PREREQ=$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
: ${ENABLE_ERIC:=true}
@ -13,6 +35,13 @@ do
source $module
done
log DEBUG "sourcing ccp/modules/exporter-setup.sh"
source ccp/modules/exporter-setup.sh
log DEBUG "sourcing ccp/modules/teiler-setup.sh"
source ccp/modules/teiler-setup.sh
SUPPORT_EMAIL=$ERIC_SUPPORT_EMAIL
BROKER_URL_FOR_PREREQ="${ERIC_BROKER_URL:-$GBN_BROKER_URL}"

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@ -69,7 +69,7 @@ loadVars() {
if [ "$(git rev-parse --abbrev-ref HEAD)" == "main" ]; then
ENVIRONMENT="production"
else
ENVIRONMENT="test"
ENVIRONMENT="test" # we have acceptance environment in BBMRI ERIC and it would be more appropriate to default to that one in case the data they have in BH is real, but I'm gonna leave it as is for backward compatibility
fi
fi
# Source the versions of the images components
@ -80,6 +80,9 @@ loadVars() {
"test")
source ./versions/test
;;
"acceptance")
source ./versions/acceptance
;;
*)
report_error 7 "Environment \"$ENVIRONMENT\" is unknown. Assuming production. FIX THIS!"
source ./versions/prod

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@ -2,13 +2,14 @@ version: "3.7"
services:
blaze:
image: docker.verbis.dkfz.de/cache/samply/blaze:0.31
image: docker.verbis.dkfz.de/cache/samply/blaze:${BLAZE_TAG}
container_name: bridgehead-cce-blaze
environment:
BASE_URL: "http://bridgehead-cce-blaze:8080"
JAVA_TOOL_OPTIONS: "-Xmx${BLAZE_MEMORY_CAP:-4096}m"
DB_RESOURCE_CACHE_SIZE: ${BLAZE_RESOURCE_CACHE_CAP:-2500000}
DB_BLOCK_CACHE_SIZE: $BLAZE_MEMORY_CAP
DB_BLOCK_CACHE_SIZE: ${BLAZE_MEMORY_CAP}
CQL_EXPR_CACHE_SIZE: ${BLAZE_CQL_CACHE_CAP:-32}
ENFORCE_REFERENTIAL_INTEGRITY: "false"
volumes:
- "blaze-data:/app/data"
@ -31,6 +32,10 @@ services:
BEAM_PROXY_URL: http://beam-proxy:8081
RETRY_COUNT: ${FOCUS_RETRY_COUNT}
EPSILON: 0.28
QUERIES_TO_CACHE: '/queries_to_cache.conf'
ENDPOINT_TYPE: ${FOCUS_ENDPOINT_TYPE:-blaze}
volumes:
- /srv/docker/bridgehead/cce/queries_to_cache.conf:/queries_to_cache.conf:ro
depends_on:
- "beam-proxy"
- "blaze"

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@ -0,0 +1,2 @@
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@ -2,7 +2,7 @@ version: "3.7"
services:
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
environment:
BASE_URL: "http://bridgehead-ccp-blaze:8080"
@ -35,7 +35,7 @@ services:
QUERIES_TO_CACHE: '/queries_to_cache.conf'
ENDPOINT_TYPE: ${FOCUS_ENDPOINT_TYPE:-blaze}
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:ro
depends_on:
- "beam-proxy"
- "blaze"

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@ -2,7 +2,7 @@ version: "3.7"
services:
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
environment:
BASE_URL: "http://bridgehead-ccp-blaze-secondary:8080"

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@ -3,7 +3,7 @@ version: "3.7"
services:
exporter:
image: docker.verbis.dkfz.de/ccp/dktk-exporter:latest
container_name: bridgehead-ccp-exporter
container_name: bridgehead-${PLATFORM}-exporter
environment:
JAVA_OPTS: "-Xms1G -Xmx8G -XX:+UseG1GC"
LOG_LEVEL: "INFO"
@ -12,39 +12,39 @@ services:
EXPORTER_DB_USER: "exporter"
EXPORTER_DB_PASSWORD: "${EXPORTER_DB_PASSWORD}" # Set in exporter-setup.sh
EXPORTER_DB_URL: "jdbc:postgresql://exporter-db:5432/exporter"
HTTP_RELATIVE_PATH: "/ccp-exporter"
HTTP_RELATIVE_PATH: "/${PLATFORM}-exporter"
SITE: "${SITE_ID}"
HTTP_SERVLET_REQUEST_SCHEME: "https"
OPAL_PASSWORD: "${EXPORTER_OPAL_PASSWORD}"
labels:
- "traefik.enable=true"
- "traefik.http.routers.exporter_ccp.rule=PathPrefix(`/ccp-exporter`)"
- "traefik.http.services.exporter_ccp.loadbalancer.server.port=8092"
- "traefik.http.routers.exporter_ccp.tls=true"
- "traefik.http.middlewares.exporter_ccp_strip.stripprefix.prefixes=/ccp-exporter"
- "traefik.http.routers.exporter_ccp.middlewares=exporter_ccp_strip"
- "traefik.http.routers.exporter_${PLATFORM}.rule=PathPrefix(`/${PLATFORM}-exporter`)"
- "traefik.http.services.exporter_${PLATFORM}.loadbalancer.server.port=8092"
- "traefik.http.routers.exporter_${PLATFORM}.tls=true"
- "traefik.http.middlewares.exporter_${PLATFORM}_strip.stripprefix.prefixes=/${PLATFORM}-exporter"
- "traefik.http.routers.exporter_${PLATFORM}.middlewares=exporter_${PLATFORM}_strip"
volumes:
- "/var/cache/bridgehead/ccp/exporter-files:/app/exporter-files/output"
- "/var/cache/bridgehead/${PLATFORM}/exporter-files:/app/exporter-files/output"
exporter-db:
image: docker.verbis.dkfz.de/cache/postgres:${POSTGRES_TAG}
container_name: bridgehead-ccp-exporter-db
container_name: bridgehead-${PLATFORM}-exporter-db
environment:
POSTGRES_USER: "exporter"
POSTGRES_PASSWORD: "${EXPORTER_DB_PASSWORD}" # Set in exporter-setup.sh
POSTGRES_DB: "exporter"
volumes:
# Consider removing this volume once we find a solution to save Lens-queries to be executed in the explorer.
- "/var/cache/bridgehead/ccp/exporter-db:/var/lib/postgresql/data"
- "/var/cache/bridgehead/${PLATFORM}/exporter-db:/var/lib/postgresql/data"
reporter:
image: docker.verbis.dkfz.de/ccp/dktk-reporter:latest
container_name: bridgehead-ccp-reporter
container_name: bridgehead-${PLATFORM}-reporter
environment:
JAVA_OPTS: "-Xms1G -Xmx8G -XX:+UseG1GC"
LOG_LEVEL: "INFO"
CROSS_ORIGINS: "https://${HOST}"
HTTP_RELATIVE_PATH: "/ccp-reporter"
HTTP_RELATIVE_PATH: "/${PLATFORM}-reporter"
SITE: "${SITE_ID}"
EXPORTER_API_KEY: "${EXPORTER_API_KEY}" # Set in exporter-setup.sh
EXPORTER_URL: "http://exporter:8092"
@ -57,14 +57,15 @@ services:
# There is a risk that the bridgehead restarts, losing the already created export.
volumes:
- "/var/cache/bridgehead/ccp/reporter-files:/app/reports"
- "/var/cache/bridgehead/${PLATFORM}/reporter-files:/app/reports"
labels:
- "traefik.enable=true"
- "traefik.http.routers.reporter_ccp.rule=PathPrefix(`/ccp-reporter`)"
- "traefik.http.services.reporter_ccp.loadbalancer.server.port=8095"
- "traefik.http.routers.reporter_ccp.tls=true"
- "traefik.http.middlewares.reporter_ccp_strip.stripprefix.prefixes=/ccp-reporter"
- "traefik.http.routers.reporter_ccp.middlewares=reporter_ccp_strip"
- "traefik.http.routers.reporter_${PLATFORM}.rule=PathPrefix(`/${PLATFORM}-reporter`)"
- "traefik.http.services.reporter_${PLATFORM}.loadbalancer.server.port=8095"
- "traefik.http.routers.reporter_${PLATFORM}.tls=true"
- "traefik.http.middlewares.reporter_${PLATFORM}_strip.stripprefix.prefixes=/${PLATFORM}-reporter"
- "traefik.http.routers.reporter_${PLATFORM}.middlewares=reporter_${PLATFORM}_strip"
focus:
environment:

View File

@ -2,7 +2,7 @@
if [ "$ENABLE_EXPORTER" == true ]; then
log INFO "Exporter setup detected -- will start Exporter service."
OVERRIDE+=" -f ./$PROJECT/modules/exporter-compose.yml"
OVERRIDE+=" -f ./ccp/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

View File

@ -3,7 +3,7 @@ version: "3.7"
services:
obds2fhir-rest:
container_name: bridgehead-obds2fhir-rest
image: docker.verbis.dkfz.de/ccp/obds2fhir-rest:main
image: docker.verbis.dkfz.de/samply/obds2fhir-rest:main
environment:
IDTYPE: BK_${IDMANAGEMENT_FRIENDLY_ID}_L-ID
MAINZELLISTE_APIKEY: ${IDMANAGER_LOCAL_PATIENTLIST_APIKEY}

View File

@ -7,30 +7,31 @@ services:
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"
- "traefik.http.routers.teiler_orchestrator_${PLATFORM}.rule=PathPrefix(`/${PLATFORM}-teiler`)"
- "traefik.http.services.teiler_orchestrator_${PLATFORM}.loadbalancer.server.port=9000"
- "traefik.http.routers.teiler_orchestrator_${PLATFORM}.tls=true"
- "traefik.http.middlewares.teiler_orchestrator_${PLATFORM}_strip.stripprefix.prefixes=/${PLATFORM}-teiler"
- "traefik.http.routers.teiler_orchestrator_${PLATFORM}.middlewares=teiler_orchestrator_${PLATFORM}_strip"
environment:
TEILER_BACKEND_URL: "https://${HOST}/ccp-teiler-backend"
TEILER_DASHBOARD_URL: "https://${HOST}/ccp-teiler-dashboard"
DEFAULT_LANGUAGE: "${TEILER_DEFAULT_LANGUAGE_LOWER_CASE}"
HTTP_RELATIVE_PATH: "/ccp-teiler"
TEILER_BACKEND_URL: "https://${HOST}/${PLATFORM}-teiler-backend"
TEILER_DASHBOARD_URL: "https://${HOST}/${PLATFORM}-teiler-dashboard"
DEFAULT_LANGUAGE: "${DEFAULT_LANGUAGE_LOWER_CASE}"
HTTP_RELATIVE_PATH: "/${PLATFORM}-teiler"
teiler-dashboard:
image: docker.verbis.dkfz.de/cache/samply/teiler-dashboard:develop
container_name: bridgehead-teiler-dashboard
labels:
- "traefik.enable=true"
- "traefik.http.routers.teiler_dashboard_ccp.rule=PathPrefix(`/ccp-teiler-dashboard`)"
- "traefik.http.services.teiler_dashboard_ccp.loadbalancer.server.port=80"
- "traefik.http.routers.teiler_dashboard_ccp.tls=true"
- "traefik.http.middlewares.teiler_dashboard_ccp_strip.stripprefix.prefixes=/ccp-teiler-dashboard"
- "traefik.http.routers.teiler_dashboard_ccp.middlewares=teiler_dashboard_ccp_strip"
- "traefik.http.routers.teiler_dashboard_${PLATFORM}.rule=PathPrefix(`/${PLATFORM}-teiler-dashboard`)"
- "traefik.http.services.teiler_dashboard_${PLATFORM}.loadbalancer.server.port=80"
- "traefik.http.routers.teiler_dashboard_${PLATFORM}.tls=true"
- "traefik.http.middlewares.teiler_dashboard_${PLATFORM}_strip.stripprefix.prefixes=/${PLATFORM}-teiler-dashboard"
- "traefik.http.routers.teiler_dashboard_${PLATFORM}.middlewares=teiler_dashboard_${PLATFORM}_strip"
environment:
DEFAULT_LANGUAGE: "${TEILER_DEFAULT_LANGUAGE}"
TEILER_BACKEND_URL: "https://${HOST}/ccp-teiler-backend"
DEFAULT_LANGUAGE: "${DEFAULT_LANGUAGE}"
TEILER_BACKEND_URL: "https://${HOST}/${PLATFORM}-teiler-backend"
TEILER_DASHBOARD_URL: "https://${HOST}/${PLATFORM}-teiler-dashboard"
OIDC_URL: "${OIDC_URL}"
OIDC_REALM: "${OIDC_REALM}"
OIDC_CLIENT_ID: "${OIDC_PUBLIC_CLIENT_ID}"
@ -40,42 +41,40 @@ services:
TEILER_ADMIN_PHONE: "${OPERATOR_PHONE}"
TEILER_PROJECT: "${PROJECT}"
EXPORTER_API_KEY: "${EXPORTER_API_KEY}"
TEILER_ORCHESTRATOR_URL: "https://${HOST}/ccp-teiler"
TEILER_DASHBOARD_HTTP_RELATIVE_PATH: "/ccp-teiler-dashboard"
TEILER_ORCHESTRATOR_HTTP_RELATIVE_PATH: "/ccp-teiler"
TEILER_ORCHESTRATOR_URL: "https://${HOST}/${PLATFORM}-teiler"
TEILER_ORCHESTRATOR_HTTP_RELATIVE_PATH: "/${PLATFORM}-teiler"
TEILER_USER: "${OIDC_USER_GROUP}"
TEILER_ADMIN: "${OIDC_ADMIN_GROUP}"
REPORTER_DEFAULT_TEMPLATE_ID: "ccp-qb"
EXPORTER_DEFAULT_TEMPLATE_ID: "ccp"
REPORTER_DEFAULT_TEMPLATE_ID: "${PLATFORM}-qb"
EXPORTER_DEFAULT_TEMPLATE_ID: "${PLATFORM}"
teiler-backend:
image: docker.verbis.dkfz.de/ccp/dktk-teiler-backend:latest
image: docker.verbis.dkfz.de/ccp/${PROJECT}-teiler-backend:latest
container_name: bridgehead-teiler-backend
labels:
- "traefik.enable=true"
- "traefik.http.routers.teiler_backend_ccp.rule=PathPrefix(`/ccp-teiler-backend`)"
- "traefik.http.services.teiler_backend_ccp.loadbalancer.server.port=8085"
- "traefik.http.routers.teiler_backend_ccp.tls=true"
- "traefik.http.middlewares.teiler_backend_ccp_strip.stripprefix.prefixes=/ccp-teiler-backend"
- "traefik.http.routers.teiler_backend_ccp.middlewares=teiler_backend_ccp_strip"
- "traefik.http.routers.teiler_backend_${PLATFORM}.rule=PathPrefix(`/${PLATFORM}-teiler-backend`)"
- "traefik.http.services.teiler_backend_${PLATFORM}.loadbalancer.server.port=8085"
- "traefik.http.routers.teiler_backend_${PLATFORM}.tls=true"
- "traefik.http.middlewares.teiler_backend_${PLATFORM}_strip.stripprefix.prefixes=/${PLATFORM}-teiler-backend"
- "traefik.http.routers.teiler_backend_${PLATFORM}.middlewares=teiler_backend_${PLATFORM}_strip"
environment:
LOG_LEVEL: "INFO"
APPLICATION_PORT: "8085"
APPLICATION_ADDRESS: "${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: "${CENTRAXX_URL}"
DEFAULT_LANGUAGE: "${DEFAULT_LANGUAGE}"
CONFIG_ENV_VAR_PATH: "/run/secrets/project-conf"
TEILER_ORCHESTRATOR_HTTP_RELATIVE_PATH: "/${PLATFORM}-teiler"
TEILER_ORCHESTRATOR_URL: "https://${HOST}/${PLATFORM}-teiler"
TEILER_DASHBOARD_DE_URL: "https://${HOST}/${PLATFORM}-teiler-dashboard/de"
TEILER_DASHBOARD_EN_URL: "https://${HOST}/${PLATFORM}-teiler-dashboard/en"
HTTP_PROXY: "http://forward_proxy:3128"
ENABLE_MTBA: "${ENABLE_MTBA}"
ENABLE_DATASHIELD: "${ENABLE_DATASHIELD}"
secrets:
- ccp.conf
- project-conf
secrets:
ccp.conf:
file: /etc/bridgehead/ccp.conf
project-conf:
file: "/etc/bridgehead/${PROJECT}.conf"

View File

@ -2,8 +2,6 @@
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,,}
OVERRIDE+=" -f ./ccp/modules/teiler-compose.yml"
add_public_oidc_redirect_url "/ccp-teiler/*"
fi

View File

@ -1,2 +1,2 @@
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View File

@ -1,3 +1,6 @@
DEFAULT_LANGUAGE=EN
DEFAULT_LANGUAGE_LOWER_CASE=${DEFAULT_LANGUAGE,,}
BROKER_ID=broker.ccp-it.dktk.dkfz.de
BROKER_URL=https://${BROKER_ID}
PROXY_ID=${SITE_ID}.${BROKER_ID}
@ -5,6 +8,7 @@ FOCUS_BEAM_SECRET_SHORT="$(cat /proc/sys/kernel/random/uuid | sed 's/[-]//g' | h
FOCUS_RETRY_COUNT=${FOCUS_RETRY_COUNT:-64}
SUPPORT_EMAIL=support-ccp@dkfz-heidelberg.de
PRIVATEKEYFILENAME=/etc/bridgehead/pki/${SITE_ID}.priv.pem
PLATFORM=bbmri
BROKER_URL_FOR_PREREQ=$BROKER_URL
@ -29,4 +33,12 @@ done
idManagementSetup
mtbaSetup
obds2fhirRestSetup
blazeSecondarySetup
blazeSecondarySetup
for module in modules/*.sh
do
log DEBUG "sourcing $module"
source $module
done
transfairSetup

View File

@ -2,7 +2,7 @@ version: "3.7"
services:
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
environment:
BASE_URL: "http://bridgehead-dhki-blaze:8080"
@ -33,7 +33,7 @@ services:
EPSILON: 0.28
QUERIES_TO_CACHE: '/queries_to_cache.conf'
volumes:
- /srv/docker/bridgehead/dhki/queries_to_cache.conf:/queries_to_cache.conf
- /srv/docker/bridgehead/dhki/queries_to_cache.conf:/queries_to_cache.conf:ro
depends_on:
- "beam-proxy"
- "blaze"

View File

@ -17,4 +17,12 @@ do
done
idManagementSetup
obds2fhirRestSetup
obds2fhirRestSetup
for module in modules/*.sh
do
log DEBUG "sourcing $module"
source $module
done
transfairSetup

View File

@ -2,13 +2,14 @@ version: "3.7"
services:
blaze:
image: docker.verbis.dkfz.de/cache/samply/blaze:0.31
image: docker.verbis.dkfz.de/cache/samply/blaze:${BLAZE_TAG}
container_name: bridgehead-itcc-blaze
environment:
BASE_URL: "http://bridgehead-itcc-blaze:8080"
JAVA_TOOL_OPTIONS: "-Xmx${BLAZE_MEMORY_CAP:-4096}m"
DB_RESOURCE_CACHE_SIZE: ${BLAZE_RESOURCE_CACHE_CAP:-2500000}
DB_BLOCK_CACHE_SIZE: $BLAZE_MEMORY_CAP
DB_BLOCK_CACHE_SIZE: ${BLAZE_MEMORY_CAP}
CQL_EXPR_CACHE_SIZE: ${BLAZE_CQL_CACHE_CAP:-32}
ENFORCE_REFERENTIAL_INTEGRITY: "false"
volumes:
- "blaze-data:/app/data"
@ -31,6 +32,10 @@ services:
BEAM_PROXY_URL: http://beam-proxy:8081
RETRY_COUNT: ${FOCUS_RETRY_COUNT}
EPSILON: 0.28
QUERIES_TO_CACHE: '/queries_to_cache.conf'
ENDPOINT_TYPE: ${FOCUS_ENDPOINT_TYPE:-blaze}
volumes:
- /srv/docker/bridgehead/itcc/queries_to_cache.conf:/queries_to_cache.conf:ro
depends_on:
- "beam-proxy"
- "blaze"

View File

@ -0,0 +1,2 @@
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

View File

@ -6,7 +6,7 @@ services:
replicas: 0 #deactivate landing page
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
environment:
BASE_URL: "http://bridgehead-kr-blaze:8080"

View File

@ -15,7 +15,7 @@ services:
environment:
TEILER_BACKEND_URL: "https://${HOST}/ccp-teiler-backend"
TEILER_DASHBOARD_URL: "https://${HOST}/ccp-teiler-dashboard"
DEFAULT_LANGUAGE: "${TEILER_DEFAULT_LANGUAGE_LOWER_CASE}"
DEFAULT_LANGUAGE: "${DEFAULT_LANGUAGE_LOWER_CASE}"
HTTP_RELATIVE_PATH: "/ccp-teiler"
teiler-dashboard:
@ -29,8 +29,9 @@ services:
- "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: "${TEILER_DEFAULT_LANGUAGE}"
DEFAULT_LANGUAGE: "${DEFAULT_LANGUAGE}"
TEILER_BACKEND_URL: "https://${HOST}/ccp-teiler-backend"
TEILER_DASHBOARD_URL: "https://${HOST}/ccp-teiler-dashboard"
OIDC_URL: "${OIDC_URL}"
OIDC_REALM: "${OIDC_REALM}"
OIDC_CLIENT_ID: "${OIDC_PUBLIC_CLIENT_ID}"
@ -41,7 +42,6 @@ services:
TEILER_PROJECT: "${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}"
@ -63,13 +63,12 @@ services:
LOG_LEVEL: "INFO"
APPLICATION_PORT: "8085"
APPLICATION_ADDRESS: "${HOST}"
DEFAULT_LANGUAGE: "${TEILER_DEFAULT_LANGUAGE}"
DEFAULT_LANGUAGE: "${DEFAULT_LANGUAGE}"
CONFIG_ENV_VAR_PATH: "/run/secrets/ccp.conf"
TEILER_ORCHESTRATOR_HTTP_RELATIVE_PATH: "/ccp-teiler"
TEILER_ORCHESTRATOR_URL: "https://${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}"

View File

@ -3,7 +3,5 @@
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 "/ccp-teiler/*"
fi

View File

@ -313,7 +313,7 @@ function sync_secrets() {
-e ALL_PROXY=$HTTPS_PROXY_FULL_URL \
-e PROXY_ID=$PROXY_ID \
-e BROKER_URL=$BROKER_URL \
-e OIDC_PROVIDER=secret-sync-central.oidc-client-enrollment.$BROKER_ID \
-e OIDC_PROVIDER=secret-sync-central.central-secret-sync.$BROKER_ID \
-e SECRET_DEFINITIONS=$secret_sync_args \
docker.verbis.dkfz.de/cache/samply/secret-sync-local:latest
@ -322,6 +322,73 @@ function sync_secrets() {
set +a # Export variables in the regular way
}
function secret_sync_gitlab_token() {
# Map the origin of the git repository /etc/bridgehead to the prefix recognized by Secret Sync
local gitlab
case "$(git -C /etc/bridgehead remote get-url origin)" in
*git.verbis.dkfz.de*) gitlab=verbis;;
*gitlab.bbmri-eric.eu*) gitlab=bbmri;;
*)
log "WARN" "Not running Secret Sync because the git repository /etc/bridgehead has unknown origin"
return
;;
esac
if [ "$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
# 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 $secret_sync_tempdir/cache.
# If it is missing or expired, Secret Sync will create a new token and write it to the file.
# The git credential helper reads the token from the file during git pull.
log "INFO" "Running Secret Sync for the GitLab token (gitlab=$gitlab)"
docker pull docker.verbis.dkfz.de/cache/samply/secret-sync-local:latest # make sure we have the latest image
docker run --rm \
-v $PRIVATEKEYFILENAME:/run/secrets/privkey.pem:ro \
-v $root_crt_file:/run/secrets/root.crt.pem:ro \
-v /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro \
-v $secret_sync_tempdir:/secret-sync/ \
-e CACHE_PATH=/secret-sync/gitlab-token \
-e TLS_CA_CERTIFICATES_DIR=/conf/trusted-ca-certs \
-e NO_PROXY=localhost,127.0.0.1 \
-e ALL_PROXY=$HTTPS_PROXY_FULL_URL \
-e PROXY_ID=$proxy_id \
-e BROKER_URL=$broker_url \
-e GITLAB_PROJECT_ACCESS_TOKEN_PROVIDER=secret-sync-central.central-secret-sync.$broker_id \
-e SECRET_DEFINITIONS=GitLabProjectAccessToken:BRIDGEHEAD_CONFIG_REPO_TOKEN:$gitlab \
docker.verbis.dkfz.de/cache/samply/secret-sync-local:latest
if [ $? -eq 0 ]; then
log "INFO" "Secret Sync was successful"
# In the past we used to hardcode tokens into the repository URL. We have to remove those now for the git credential helper to become effective.
CLEAN_REPO="$(git -C /etc/bridgehead remote get-url origin | sed -E 's|https://[^@]+@|https://|')"
git -C /etc/bridgehead remote set-url origin "$CLEAN_REPO"
# Set the git credential helper
git -C /etc/bridgehead config credential.helper /srv/docker/bridgehead/lib/gitlab-token-helper.sh
else
log "WARN" "Secret Sync failed"
# Remove the git credential helper
git -C /etc/bridgehead config --unset credential.helper
fi
# In the past the git credential helper was also set for /srv/docker/bridgehead but never used.
# Let's remove it to avoid confusion. This line can be removed at some point the future when we
# believe that it was removed on all/most production servers.
git -C /srv/docker/bridgehead config --unset credential.helper
}
capitalize_first_letter() {
input="$1"
capitalized="$(tr '[:lower:]' '[:upper:]' <<< ${input:0:1})${input:1}"

View File

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

View File

@ -41,6 +41,14 @@ if [ ! -z "$NNGM_CTS_APIKEY" ] && [ -z "$NNGM_AUTH" ]; then
add_basic_auth_user "nngm" $generated_passwd "NNGM_AUTH" $PROJECT
fi
if [ -z "$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"
cp -v \
lib/systemd/bridgehead\@.service \

View File

@ -33,43 +33,7 @@ export SITE_ID
checkOwner /srv/docker/bridgehead bridgehead || fail_and_report 1 "Update failed: Wrong permissions in /srv/docker/bridgehead"
checkOwner /etc/bridgehead bridgehead || fail_and_report 1 "Update failed: Wrong permissions in /etc/bridgehead"
# 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.
# 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"
docker pull docker.verbis.dkfz.de/cache/samply/secret-sync-local:latest # make sure we have the latest image
docker run --rm \
-v /var/cache/bridgehead/secrets/gitlab_token:/usr/local/cache \
-v $PRIVATEKEYFILENAME:/run/secrets/privkey.pem:ro \
-v /srv/docker/bridgehead/$PROJECT/root.crt.pem:/run/secrets/root.crt.pem:ro \
-v /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro \
-e TLS_CA_CERTIFICATES_DIR=/conf/trusted-ca-certs \
-e NO_PROXY=localhost,127.0.0.1 \
-e ALL_PROXY=$HTTPS_PROXY_FULL_URL \
-e PROXY_ID=$PROXY_ID \
-e BROKER_URL=$BROKER_URL \
-e GITLAB_PROJECT_ACCESS_TOKEN_PROVIDER=secret-sync-central.oidc-client-enrollment.$BROKER_ID \
-e SECRET_DEFINITIONS=GitLabProjectAccessToken:BRIDGEHEAD_CONFIG_REPO_TOKEN: \
docker.verbis.dkfz.de/cache/samply/secret-sync-local:latest
if [ $? -eq 0 ]; then
log "INFO" "Secret Sync was successful"
# In the past we used to hardcode tokens into the repository URL. We have to remove those now for the git credential helper to become effective.
CLEAN_REPO="$(git -C /etc/bridgehead remote get-url origin | sed -E 's|https://[^@]+@|https://|')"
git -C /etc/bridgehead remote set-url origin "$CLEAN_REPO"
# Set the git credential helper
git -C /etc/bridgehead config credential.helper /srv/docker/bridgehead/lib/gitlab-token-helper.sh
else
log "WARN" "Secret Sync failed"
# Remove the git credential helper
git -C /etc/bridgehead config --unset credential.helper
fi
# In the past the git credential helper was also set for /srv/docker/bridgehead but never used.
# Let's remove it to avoid confusion. This line can be removed at some point the future when we
# believe that it was removed on all/most production servers.
git -C /srv/docker/bridgehead config --unset credential.helper
secret_sync_gitlab_token
CHANGES=""

View 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

View 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 ./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!**

View File

@ -0,0 +1,86 @@
services:
transfair:
image: docker.verbis.dkfz.de/cache/samply/transfair:latest
container_name: bridgehead-transfair
environment:
# NOTE: Those 3 variables need only to be passed if their set, otherwise transfair will complain about empty url values
- TTP_URL
- TTP_ML_API_KEY
- TTP_GW_SOURCE
- TTP_GW_EPIX_DOMAIN
- TTP_GW_GPAS_DOMAIN
- TTP_TYPE
- TTP_AUTH
- PROJECT_ID_SYSTEM
- FHIR_REQUEST_URL=${FHIR_REQUEST_URL}
- FHIR_INPUT_URL=${FHIR_INPUT_URL}
- FHIR_OUTPUT_URL=${FHIR_OUTPUT_URL:-http://blaze:8080}
- FHIR_REQUEST_CREDENTIALS=${FHIR_REQUEST_CREDENTIALS}
- FHIR_INPUT_CREDENTIALS=${FHIR_INPUT_CREDENTIALS}
- FHIR_OUTPUT_CREDENTIALS=${FHIR_OUTPUT_CREDENTIALS}
- EXCHANGE_ID_SYSTEM=${EXCHANGE_ID_SYSTEM:-SESSION_ID}
- DATABASE_URL=sqlite://transfair/data_requests.sql?mode=rwc
- RUST_LOG=${RUST_LOG:-info}
- TLS_CA_CERTIFICATES_DIR=/conf/trusted-ca-certs
- TLS_DISABLE=${TRANSFAIR_TLS_DISABLE:-false}
- NO_PROXY=${TRANSFAIR_NO_PROXIES}
- ALL_PROXY=http://forward_proxy:3128
volumes:
- /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:
image: docker.verbis.dkfz.de/cache/samply/blaze:${BLAZE_TAG}
container_name: bridgehead-transfair-input-blaze
environment:
BASE_URL: "http://bridgehead-transfair-input-blaze:8080"
JAVA_TOOL_OPTIONS: "-Xmx1024m"
DB_BLOCK_CACHE_SIZE: 1024
CQL_EXPR_CACHE_SIZE: 8
ENFORCE_REFERENTIAL_INTEGRITY: "false"
volumes:
- "transfair-input-blaze-data:/app/data"
profiles: ["transfair-input-blaze"]
labels:
- "traefik.enable=true"
- "traefik.http.routers.transfair-input-blaze.rule=PathPrefix(`/data-delivery`)"
- "traefik.http.middlewares.transfair-input-strip.stripprefix.prefixes=/data-delivery"
- "traefik.http.services.transfair-input-blaze.loadbalancer.server.port=8080"
- "traefik.http.routers.transfair-input-blaze.middlewares=transfair-input-strip,transfair-auth"
- "traefik.http.routers.transfair-input-blaze.tls=true"
transfair-request-blaze:
image: docker.verbis.dkfz.de/cache/samply/blaze:${BLAZE_TAG}
container_name: bridgehead-transfair-request-blaze
environment:
BASE_URL: "http://bridgehead-transfair-request-blaze:8080"
JAVA_TOOL_OPTIONS: "-Xmx1024m"
DB_BLOCK_CACHE_SIZE: 1024
CQL_EXPR_CACHE_SIZE: 8
ENFORCE_REFERENTIAL_INTEGRITY: "false"
volumes:
- "transfair-request-blaze-data:/app/data"
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:
transfair-input-blaze-data:
transfair-request-blaze-data:

35
modules/transfair-setup.sh Executable file
View File

@ -0,0 +1,35 @@
#!/bin/bash -e
function transfairSetup() {
if [[ -n "$TTP_URL" || -n "$EXCHANGE_ID_SYSTEM" ]]; then
echo "Starting transfair."
OVERRIDE+=" -f ./modules/transfair-compose.yml"
if [ -n "$FHIR_INPUT_URL" ]; then
log INFO "TransFAIR input fhir store set to external $FHIR_INPUT_URL"
else
log INFO "TransFAIR input fhir store not set writing to internal blaze"
FHIR_INPUT_URL="http://transfair-input-blaze:8080"
OVERRIDE+=" --profile transfair-input-blaze"
fi
if [ -n "$FHIR_REQUEST_URL" ]; then
log INFO "TransFAIR request fhir store set to external $FHIR_REQUEST_URL"
else
log INFO "TransFAIR request fhir store not set writing to internal blaze"
FHIR_REQUEST_URL="http://transfair-request-blaze:8080"
OVERRIDE+=" --profile transfair-request-blaze"
fi
if [ -n "$TTP_GW_SOURCE" ]; then
log INFO "TransFAIR configured with greifswald as ttp"
TTP_TYPE="greifswald"
elif [ -n "$TTP_ML_API_KEY" ]; then
log INFO "TransFAIR configured with mainzelliste as ttp"
TTP_TYPE="mainzelliste"
else
log INFO "TransFAIR configured without ttp"
fi
TRANSFAIR_NO_PROXIES="transfair-input-blaze,blaze,transfair-requests-blaze"
if [ -n "${TRANSFAIR_NO_PROXY}" ]; then
TRANSFAIR_NO_PROXIES+=",${TRANSFAIR_NO_PROXY}"
fi
fi
}

3
versions/acceptance Normal file
View File

@ -0,0 +1,3 @@
FOCUS_TAG=develop
BEAM_TAG=develop
BLAZE_TAG=main

View File

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

View File

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