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https://github.com/samply/bridgehead.git
synced 2025-06-16 17:20:15 +02:00
Compare commits
43 Commits
feat/routi
...
qr-bbmri-v
Author | SHA1 | Date | |
---|---|---|---|
ae80e6bb9d | |||
6476529abd | |||
af08a9fb08 | |||
b95f0efbe7 | |||
99567e2b40 | |||
96ff6043a1 | |||
844ce3386e | |||
9782bf66b6 | |||
87f0e8ad7f | |||
7365be3e7b | |||
c5d08c50a4 | |||
72ecaadba8 | |||
2ddd535794 | |||
973547c322 | |||
6b649c9233 | |||
3144ee5214 | |||
68804dc71b | |||
e5aebfe382 | |||
6f3aba1eaa | |||
82ced89b33 | |||
5d94bac0e2 | |||
83555540f5 | |||
e396e00178 | |||
ecb29830e4 | |||
98121c17e8 | |||
e38511e118 | |||
8334fac84d | |||
8000356b57 | |||
74d8e68d96 | |||
721627a78f | |||
e08ff92401 | |||
e3553370b6 | |||
1ad73d8f82 | |||
0b6fa439ba | |||
615990b92a | |||
db950d6d87 | |||
6a71da3dd1 | |||
138a1fa5f1 | |||
39a87bcf61 | |||
655d0d24c7 | |||
df1ec21848 | |||
a4e292dd18 | |||
75089ab428 |
1
.github/CODEOWNERS
vendored
Normal file
1
.github/CODEOWNERS
vendored
Normal file
@ -0,0 +1 @@
|
||||
* @samply/bridgehead-developers
|
@ -76,7 +76,7 @@ The following URLs need to be accessible (prefix with `https://`):
|
||||
* git.verbis.dkfz.de
|
||||
* To fetch docker images
|
||||
* docker.verbis.dkfz.de
|
||||
* Official Docker, Inc. URLs (subject to change, see [official list](https://docs.docker.com/desktop/all))
|
||||
* Official Docker, Inc. URLs (subject to change, see [official list](https://docs.docker.com/desktop/setup/allow-list/))
|
||||
* hub.docker.com
|
||||
* registry-1.docker.io
|
||||
* production.cloudflare.docker.com
|
||||
@ -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:
|
||||
|
@ -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:${BLAZE_TAG}
|
||||
container_name: bridgehead-bbmri-blaze
|
||||
environment:
|
||||
BASE_URL: "http://bridgehead-bbmri-blaze:8080"
|
||||
|
@ -10,6 +10,10 @@ if [ "${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
|
||||
|
20
bbmri/modules/eric.acc.root.crt.pem
Normal file
20
bbmri/modules/eric.acc.root.crt.pem
Normal file
@ -0,0 +1,20 @@
|
||||
-----BEGIN CERTIFICATE-----
|
||||
MIIDNTCCAh2gAwIBAgIUE/wu6FmI+KSMOalI65b+lI3HI4cwDQYJKoZIhvcNAQEL
|
||||
BQAwFjEUMBIGA1UEAxMLQnJva2VyLVJvb3QwHhcNMjQwOTE2MTUyMzU0WhcNMzQw
|
||||
OTE0MTUyNDI0WjAWMRQwEgYDVQQDEwtCcm9rZXItUm9vdDCCASIwDQYJKoZIhvcN
|
||||
AQEBBQADggEPADCCAQoCggEBAOt1I1FQt2bI4Nnjtg8JBYid29cBIkDT4MMb45Jr
|
||||
ays24y4R3WO7VJK9UjNduSq/A1jlA0W0A/szDf8Ojq6bBtg+uL92PTDjYH1QXwX0
|
||||
c7eMo2tvvyyrs/cb2/ovDBQ1lpibcxVmVAv042ASmil3SdqKKXpv3ATnF9I7V4cv
|
||||
fwB56FChaGIov5EK+9JOMjTx6oMlBEgUFR6qq/lSqM9my0HYwUFbX2W+nT9EKEIP
|
||||
9UP1eyfRZR3E/+oticnm/cS20BGCbjoYrNgLthXKyaASuhGoElKs8EZ3h9MiI+u0
|
||||
DpR0KpePhAkMLugBrgYWqkMwwD1684LfC4YVQrsLwzo5OW8CAwEAAaN7MHkwDgYD
|
||||
VR0PAQH/BAQDAgEGMA8GA1UdEwEB/wQFMAMBAf8wHQYDVR0OBBYEFPbXs3g3lMjH
|
||||
1JMe0a5aVbN7lB92MB8GA1UdIwQYMBaAFPbXs3g3lMjH1JMe0a5aVbN7lB92MBYG
|
||||
A1UdEQQPMA2CC0Jyb2tlci1Sb290MA0GCSqGSIb3DQEBCwUAA4IBAQBM5RsXb2HN
|
||||
FpC1mYfocXAn20Zu4d603qmc/IqkiOWbp36pWo+jk1AxejyRS9hEpQalgSnvcRPQ
|
||||
1hPEhGU+wvI0WWVi/01iNjVbXmJNPQEouXQWAT17dyp9vqQkPw8LNzpSV/qdPgbT
|
||||
Z9o3sZrjUsSLsK7A7Q5ky4ePkiJBaMsHeAD+wqGwpiJ4D2Xhp8e1v36TWM0qt2EA
|
||||
gySx9isx/jeGGPBmDqYB9BCal5lrihPN56jd+5pCkyXeZqKWiiXFJKXwcwxctYZc
|
||||
ADHIiTLLPXE8LHTUJAO51it1NAZ1S24aMzax4eWDXcWO7/ybbx5pkYkMd6EqlKHd
|
||||
8riQJIhY4huX
|
||||
-----END CERTIFICATE-----
|
29
bbmri/vars
29
bbmri/vars
@ -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}"
|
||||
|
||||
|
52
bridgehead
52
bridgehead
@ -53,17 +53,47 @@ case "$PROJECT" in
|
||||
;;
|
||||
esac
|
||||
|
||||
# Loads config variables and runs the projects setup script
|
||||
loadVars() {
|
||||
# Load variables from /etc/bridgehead and /srv/docker/bridgehead
|
||||
set -a
|
||||
# Source the project specific config file
|
||||
source /etc/bridgehead/$PROJECT.conf || fail_and_report 1 "/etc/bridgehead/$PROJECT.conf not found"
|
||||
# Source the project specific local config file if present
|
||||
# This file is ignored by git as oposed to the regular config file as it contains private site information like etl auth data
|
||||
if [ -e /etc/bridgehead/$PROJECT.local.conf ]; then
|
||||
log INFO "Applying /etc/bridgehead/$PROJECT.local.conf"
|
||||
source /etc/bridgehead/$PROJECT.local.conf || fail_and_report 1 "Found /etc/bridgehead/$PROJECT.local.conf but failed to import"
|
||||
fi
|
||||
# Set execution environment on main default to prod else test
|
||||
if [[ -z "${ENVIRONMENT+x}" ]]; then
|
||||
if [ "$(git rev-parse --abbrev-ref HEAD)" == "main" ]; then
|
||||
ENVIRONMENT="production"
|
||||
else
|
||||
ENVIRONMENT="test" # we have acceptance environment in BBMRI ERIC and it would be more appropriate to default to that one in case the data they have in BH is real, but I'm gonna leave it as is for backward compatibility
|
||||
fi
|
||||
fi
|
||||
# Source the versions of the images components
|
||||
case "$ENVIRONMENT" in
|
||||
"production")
|
||||
source ./versions/prod
|
||||
;;
|
||||
"test")
|
||||
source ./versions/test
|
||||
;;
|
||||
"acceptance")
|
||||
source ./versions/acceptance
|
||||
;;
|
||||
*)
|
||||
report_error 7 "Environment \"$ENVIRONMENT\" is unknown. Assuming production. FIX THIS!"
|
||||
source ./versions/prod
|
||||
;;
|
||||
esac
|
||||
fetchVarsFromVaultByFile /etc/bridgehead/$PROJECT.conf || fail_and_report 1 "Unable to fetchVarsFromVaultByFile"
|
||||
setHostname
|
||||
optimizeBlazeMemoryUsage
|
||||
# Run project specific setup if it exists
|
||||
# This will ususally modiy the `OVERRIDE` to include all the compose files that the project depends on
|
||||
# This is also where projects specify which modules to load
|
||||
[ -e ./$PROJECT/vars ] && source ./$PROJECT/vars
|
||||
set +a
|
||||
|
||||
@ -79,26 +109,6 @@ loadVars() {
|
||||
fi
|
||||
detectCompose
|
||||
setupProxy
|
||||
|
||||
# Set some project-independent default values
|
||||
: ${ENVIRONMENT:=production}
|
||||
export ENVIRONMENT
|
||||
|
||||
case "$ENVIRONMENT" in
|
||||
"production")
|
||||
export FOCUS_TAG=main
|
||||
export BEAM_TAG=main
|
||||
;;
|
||||
"test")
|
||||
export FOCUS_TAG=develop
|
||||
export BEAM_TAG=develop
|
||||
;;
|
||||
*)
|
||||
report_error 7 "Environment \"$ENVIRONMENT\" is unknown. Assuming production. FIX THIS!"
|
||||
export FOCUS_TAG=main
|
||||
export BEAM_TAG=main
|
||||
;;
|
||||
esac
|
||||
}
|
||||
|
||||
case "$ACTION" in
|
||||
|
@ -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: ${FOCUS_ENDPOINT_TYPE:-blaze}
|
||||
volumes:
|
||||
- /srv/docker/bridgehead/cce/queries_to_cache.conf:/queries_to_cache.conf:ro
|
||||
depends_on:
|
||||
- "beam-proxy"
|
||||
- "blaze"
|
||||
|
2
cce/queries_to_cache.conf
Normal file
2
cce/queries_to_cache.conf
Normal file
@ -0,0 +1,2 @@
|
||||
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
|
||||
bGlicmFyeSBSZXRyaWV2ZQp1c2luZyBGSElSIHZlcnNpb24gJzQuMC4wJwppbmNsdWRlIEZISVJIZWxwZXJzIHZlcnNpb24gJzQuMC4wJwpjb2Rlc3lzdGVtIFNhbXBsZU1hdGVyaWFsVHlwZTogJ2h0dHBzOi8vZmhpci5iYm1yaS5kZS9Db2RlU3lzdGVtL1NhbXBsZU1hdGVyaWFsVHlwZScKCmNvZGVzeXN0ZW0gbG9pbmM6ICdodHRwOi8vbG9pbmMub3JnJwpjb2Rlc3lzdGVtIGljZDEwOiAnaHR0cDovL2ZoaXIuZGUvQ29kZVN5c3RlbS9iZmFybS9pY2QtMTAtZ20nCmNvZGVzeXN0ZW0gbW9ycGg6ICd1cm46b2lkOjIuMTYuODQwLjEuMTEzODgzLjYuNDMuMScKCmNvbnRleHQgUGF0aWVudAoKREtUS19TVFJBVF9HRU5ERVJfU1RSQVRJRklFUgoKREtUS19TVFJBVF9BR0VfU1RSQVRJRklFUgoKREtUS19TVFJBVF9ERUNFQVNFRF9TVFJBVElGSUVSCgpES1RLX1NUUkFUX0RJQUdOT1NJU19TVFJBVElGSUVSCgpES1RLX1NUUkFUX1NQRUNJTUVOX1NUUkFUSUZJRVIKCkRLVEtfU1RSQVRfUFJPQ0VEVVJFX1NUUkFUSUZJRVIKCkRLVEtfU1RSQVRfTUVESUNBVElPTl9TVFJBVElGSUVSCkRLVEtfU1RSQVRfREVGX0lOX0lOSVRJQUxfUE9QVUxBVElPTgooKGV4aXN0cyBbQ29uZGl0aW9uOiBDb2RlICdDNjEnIGZyb20gaWNkMTBdKSBhbmQKKChleGlzdHMgZnJvbSBbT2JzZXJ2YXRpb246IENvZGUgJzU5ODQ3LTQnIGZyb20gbG9pbmNdIE8Kd2hlcmUgTy52YWx1ZS5jb2RpbmcuY29kZSBjb250YWlucyAnODE0MC8zJykgb3IKKGV4aXN0cyBmcm9tIFtPYnNlcnZhdGlvbjogQ29kZSAnNTk4NDctNCcgZnJvbSBsb2luY10gTwp3aGVyZSBPLnZhbHVlLmNvZGluZy5jb2RlIGNvbnRhaW5zICc4MTQ3LzMnKSBvcgooZXhpc3RzIGZyb20gW09ic2VydmF0aW9uOiBDb2RlICc1OTg0Ny00JyBmcm9tIGxvaW5jXSBPCndoZXJlIE8udmFsdWUuY29kaW5nLmNvZGUgY29udGFpbnMgJzg0ODAvMycpIG9yCihleGlzdHMgZnJvbSBbT2JzZXJ2YXRpb246IENvZGUgJzU5ODQ3LTQnIGZyb20gbG9pbmNdIE8Kd2hlcmUgTy52YWx1ZS5jb2RpbmcuY29kZSBjb250YWlucyAnODUwMC8zJykpKQ==
|
@ -2,7 +2,7 @@ version: "3.7"
|
||||
|
||||
services:
|
||||
blaze:
|
||||
image: docker.verbis.dkfz.de/cache/samply/blaze:0.31
|
||||
image: docker.verbis.dkfz.de/cache/samply/blaze:${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: ${FOCUS_ENDPOINT_TYPE:-blaze}
|
||||
volumes:
|
||||
- /srv/docker/bridgehead/ccp/queries_to_cache.conf:/queries_to_cache.conf
|
||||
- /srv/docker/bridgehead/ccp/queries_to_cache.conf:/queries_to_cache.conf:ro
|
||||
depends_on:
|
||||
- "beam-proxy"
|
||||
- "blaze"
|
||||
|
@ -2,7 +2,7 @@ version: "3.7"
|
||||
|
||||
services:
|
||||
blaze-secondary:
|
||||
image: docker.verbis.dkfz.de/cache/samply/blaze:0.31
|
||||
image: docker.verbis.dkfz.de/cache/samply/blaze:${BLAZE_TAG}
|
||||
container_name: bridgehead-ccp-blaze-secondary
|
||||
environment:
|
||||
BASE_URL: "http://bridgehead-ccp-blaze-secondary:8080"
|
||||
|
@ -13,7 +13,7 @@ services:
|
||||
PROXY_APIKEY: ${DNPM_BEAM_SECRET_SHORT}
|
||||
APP_ID: dnpm-connect.${PROXY_ID}
|
||||
DISCOVERY_URL: "./conf/central_targets.json"
|
||||
LOCAL_TARGETS_FILE: "./conf/connect_targets.json"
|
||||
LOCAL_TARGETS_FILE: "/conf/connect_targets.json"
|
||||
HTTP_PROXY: "http://forward_proxy:3128"
|
||||
HTTPS_PROXY: "http://forward_proxy:3128"
|
||||
NO_PROXY: beam-proxy,dnpm-backend,host.docker.internal${DNPM_ADDITIONAL_NO_PROXY}
|
||||
@ -25,7 +25,7 @@ services:
|
||||
volumes:
|
||||
- /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro
|
||||
- /etc/bridgehead/dnpm/local_targets.json:/conf/connect_targets.json:ro
|
||||
- /etc/bridgehead/dnpm/central_targets.json:/conf/central_targets.json:ro
|
||||
- /srv/docker/bridgehead/minimal/modules/dnpm-central-targets.json:/conf/central_targets.json:ro
|
||||
labels:
|
||||
- "traefik.enable=true"
|
||||
- "traefik.http.routers.dnpm-connect.rule=PathPrefix(`/dnpm-connect`)"
|
||||
|
@ -1,34 +1,99 @@
|
||||
version: "3.7"
|
||||
|
||||
services:
|
||||
dnpm-backend:
|
||||
image: ghcr.io/kohlbacherlab/bwhc-backend:1.0-snapshot-broker-connector
|
||||
container_name: bridgehead-dnpm-backend
|
||||
dnpm-mysql:
|
||||
image: mysql:9
|
||||
healthcheck:
|
||||
test: [ "CMD", "mysqladmin" ,"ping", "-h", "localhost" ]
|
||||
interval: 3s
|
||||
timeout: 5s
|
||||
retries: 5
|
||||
environment:
|
||||
- ZPM_SITE=${ZPM_SITE}
|
||||
- N_RANDOM_FILES=${DNPM_SYNTH_NUM}
|
||||
MYSQL_ROOT_HOST: "%"
|
||||
MYSQL_ROOT_PASSWORD: ${DNPM_MYSQL_ROOT_PASSWORD}
|
||||
volumes:
|
||||
- /etc/bridgehead/dnpm:/bwhc_config:ro
|
||||
- ${DNPM_DATA_DIR}:/bwhc_data
|
||||
labels:
|
||||
- "traefik.enable=true"
|
||||
- "traefik.http.routers.bwhc-backend.rule=PathPrefix(`/bwhc`)"
|
||||
- "traefik.http.services.bwhc-backend.loadbalancer.server.port=9000"
|
||||
- "traefik.http.routers.bwhc-backend.tls=true"
|
||||
- /var/cache/bridgehead/dnpm/mysql:/var/lib/mysql
|
||||
|
||||
dnpm-frontend:
|
||||
image: ghcr.io/kohlbacherlab/bwhc-frontend:2209
|
||||
container_name: bridgehead-dnpm-frontend
|
||||
links:
|
||||
- dnpm-backend
|
||||
dnpm-authup:
|
||||
image: authup/authup:latest
|
||||
container_name: bridgehead-dnpm-authup
|
||||
volumes:
|
||||
- /var/cache/bridgehead/dnpm/authup:/usr/src/app/writable
|
||||
depends_on:
|
||||
dnpm-mysql:
|
||||
condition: service_healthy
|
||||
command: server/core start
|
||||
environment:
|
||||
- NUXT_HOST=0.0.0.0
|
||||
- NUXT_PORT=8080
|
||||
- BACKEND_PROTOCOL=https
|
||||
- BACKEND_HOSTNAME=$HOST
|
||||
- BACKEND_PORT=443
|
||||
- PUBLIC_URL=https://${HOST}/auth/
|
||||
- AUTHORIZE_REDIRECT_URL=https://${HOST}
|
||||
- ROBOT_ADMIN_ENABLED=true
|
||||
- ROBOT_ADMIN_SECRET=${DNPM_AUTHUP_SECRET}
|
||||
- ROBOT_ADMIN_SECRET_RESET=true
|
||||
- DB_TYPE=mysql
|
||||
- DB_HOST=dnpm-mysql
|
||||
- DB_USERNAME=root
|
||||
- DB_PASSWORD=${DNPM_MYSQL_ROOT_PASSWORD}
|
||||
- DB_DATABASE=auth
|
||||
labels:
|
||||
- "traefik.enable=true"
|
||||
- "traefik.http.routers.bwhc-frontend.rule=PathPrefix(`/`)"
|
||||
- "traefik.http.services.bwhc-frontend.loadbalancer.server.port=8080"
|
||||
- "traefik.http.routers.bwhc-frontend.tls=true"
|
||||
- "traefik.http.middlewares.authup-strip.stripprefix.prefixes=/auth"
|
||||
- "traefik.http.routers.dnpm-auth.middlewares=authup-strip"
|
||||
- "traefik.http.routers.dnpm-auth.rule=PathPrefix(`/auth`)"
|
||||
- "traefik.http.services.dnpm-auth.loadbalancer.server.port=3000"
|
||||
- "traefik.http.routers.dnpm-auth.tls=true"
|
||||
|
||||
dnpm-portal:
|
||||
image: ghcr.io/dnpm-dip/portal:latest
|
||||
container_name: bridgehead-dnpm-portal
|
||||
environment:
|
||||
- NUXT_API_URL=http://dnpm-backend:9000/
|
||||
- NUXT_PUBLIC_API_URL=https://${HOST}/api/
|
||||
- NUXT_AUTHUP_URL=http://dnpm-authup:3000/
|
||||
- NUXT_PUBLIC_AUTHUP_URL=https://${HOST}/auth/
|
||||
labels:
|
||||
- "traefik.enable=true"
|
||||
- "traefik.http.routers.dnpm-frontend.rule=PathPrefix(`/`)"
|
||||
- "traefik.http.services.dnpm-frontend.loadbalancer.server.port=3000"
|
||||
- "traefik.http.routers.dnpm-frontend.tls=true"
|
||||
|
||||
dnpm-backend:
|
||||
container_name: bridgehead-dnpm-backend
|
||||
image: ghcr.io/dnpm-dip/backend:latest
|
||||
environment:
|
||||
- LOCAL_SITE=${ZPM_SITE}:${SITE_NAME} # Format: {Site-ID}:{Site-name}, e.g. UKT:Tübingen
|
||||
- RD_RANDOM_DATA=${DNPM_SYNTH_NUM:--1}
|
||||
- MTB_RANDOM_DATA=${DNPM_SYNTH_NUM:--1}
|
||||
- HATEOAS_HOST=https://${HOST}
|
||||
- CONNECTOR_TYPE=broker
|
||||
- AUTHUP_URL=robot://system:${DNPM_AUTHUP_SECRET}@http://dnpm-authup:3000
|
||||
volumes:
|
||||
- /etc/bridgehead/dnpm/config:/dnpm_config
|
||||
- /var/cache/bridgehead/dnpm/backend-data:/dnpm_data
|
||||
depends_on:
|
||||
dnpm-authup:
|
||||
condition: service_healthy
|
||||
labels:
|
||||
- "traefik.enable=true"
|
||||
- "traefik.http.services.dnpm-backend.loadbalancer.server.port=9000"
|
||||
# expose everything
|
||||
- "traefik.http.routers.dnpm-backend.rule=PathPrefix(`/api`)"
|
||||
- "traefik.http.routers.dnpm-backend.tls=true"
|
||||
- "traefik.http.routers.dnpm-backend.service=dnpm-backend"
|
||||
# except ETL
|
||||
- "traefik.http.routers.dnpm-backend-etl.rule=PathRegexp(`^/api(/.*)?etl(/.*)?$`)"
|
||||
- "traefik.http.routers.dnpm-backend-etl.tls=true"
|
||||
- "traefik.http.routers.dnpm-backend-etl.service=dnpm-backend"
|
||||
# this needs an ETL processor with support for basic auth
|
||||
- "traefik.http.routers.dnpm-backend-etl.middlewares=auth"
|
||||
# except peer-to-peer
|
||||
- "traefik.http.routers.dnpm-backend-peer.rule=PathRegexp(`^/api(/.*)?/peer2peer(/.*)?$`)"
|
||||
- "traefik.http.routers.dnpm-backend-peer.tls=true"
|
||||
- "traefik.http.routers.dnpm-backend-peer.service=dnpm-backend"
|
||||
- "traefik.http.routers.dnpm-backend-peer.middlewares=dnpm-backend-peer"
|
||||
# this effectively denies all requests
|
||||
# this is okay, because requests from peers don't go through Traefik
|
||||
- "traefik.http.middlewares.dnpm-backend-peer.ipWhiteList.sourceRange=0.0.0.0/32"
|
||||
|
||||
landing:
|
||||
labels:
|
||||
- "traefik.http.routers.landing.rule=PathPrefix(`/landing`)"
|
||||
|
@ -1,28 +1,16 @@
|
||||
#!/bin/bash
|
||||
|
||||
if [ -n "${ENABLE_DNPM_NODE}" ]; then
|
||||
log INFO "DNPM setup detected (BwHC Node) -- will start BwHC node."
|
||||
log INFO "DNPM setup detected -- will start DNPM:DIP node."
|
||||
OVERRIDE+=" -f ./$PROJECT/modules/dnpm-node-compose.yml"
|
||||
|
||||
# Set variables required for BwHC Node. ZPM_SITE is assumed to be set in /etc/bridgehead/<project>.conf
|
||||
DNPM_APPLICATION_SECRET="$(echo \"This is a salt string to generate one consistent password for DNPM. It is not required to be secret.\" | sha1sum | openssl pkeyutl -sign -inkey /etc/bridgehead/pki/${SITE_ID}.priv.pem | base64 | head -c 30)"
|
||||
if [ -z "${ZPM_SITE+x}" ]; then
|
||||
log ERROR "Mandatory variable ZPM_SITE not defined!"
|
||||
exit 1
|
||||
fi
|
||||
if [ -z "${DNPM_DATA_DIR+x}" ]; then
|
||||
log ERROR "Mandatory variable DNPM_DATA_DIR not defined!"
|
||||
exit 1
|
||||
fi
|
||||
DNPM_SYNTH_NUM=${DNPM_SYNTH_NUM:-0}
|
||||
if grep -q 'traefik.http.routers.landing.rule=PathPrefix(`/landing`)' /srv/docker/bridgehead/minimal/docker-compose.override.yml 2>/dev/null; then
|
||||
echo "Override of landing page url already in place"
|
||||
else
|
||||
echo "Adding override of landing page url"
|
||||
if [ -f /srv/docker/bridgehead/minimal/docker-compose.override.yml ]; then
|
||||
echo -e ' landing:\n labels:\n - "traefik.http.routers.landing.rule=PathPrefix(`/landing`)"' >> /srv/docker/bridgehead/minimal/docker-compose.override.yml
|
||||
else
|
||||
echo -e 'version: "3.7"\nservices:\n landing:\n labels:\n - "traefik.http.routers.landing.rule=PathPrefix(`/landing`)"' >> /srv/docker/bridgehead/minimal/docker-compose.override.yml
|
||||
fi
|
||||
fi
|
||||
mkdir -p /var/cache/bridgehead/dnpm/ || fail_and_report 1 "Failed to create '/var/cache/bridgehead/dnpm/'. Please run sudo './bridgehead install $PROJECT' again to fix the permissions."
|
||||
DNPM_SYNTH_NUM=${DNPM_SYNTH_NUM:--1}
|
||||
DNPM_MYSQL_ROOT_PASSWORD="$(generate_simple_password 'dnpm mysql')"
|
||||
DNPM_AUTHUP_SECRET="$(generate_simple_password 'dnpm authup')"
|
||||
fi
|
||||
|
@ -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:
|
||||
|
@ -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
|
||||
|
@ -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: ${IDMANAGER_LOCAL_PATIENTLIST_APIKEY}
|
||||
|
@ -7,30 +7,31 @@ services:
|
||||
container_name: bridgehead-teiler-orchestrator
|
||||
labels:
|
||||
- "traefik.enable=true"
|
||||
- "traefik.http.routers.teiler_orchestrator_ccp.rule=PathPrefix(`/ccp-teiler`)"
|
||||
- "traefik.http.services.teiler_orchestrator_ccp.loadbalancer.server.port=9000"
|
||||
- "traefik.http.routers.teiler_orchestrator_ccp.tls=true"
|
||||
- "traefik.http.middlewares.teiler_orchestrator_ccp_strip.stripprefix.prefixes=/ccp-teiler"
|
||||
- "traefik.http.routers.teiler_orchestrator_ccp.middlewares=teiler_orchestrator_ccp_strip"
|
||||
- "traefik.http.routers.teiler_orchestrator_${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/${PROJECT}.conf"
|
||||
|
@ -2,8 +2,6 @@
|
||||
|
||||
if [ "$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
|
||||
|
@ -1,2 +1,2 @@
|
||||
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
|
||||
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
|
||||
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
|
||||
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
|
14
ccp/vars
14
ccp/vars
@ -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 $module
|
||||
done
|
||||
|
||||
transfairSetup
|
@ -2,7 +2,7 @@ version: "3.7"
|
||||
|
||||
services:
|
||||
blaze:
|
||||
image: docker.verbis.dkfz.de/cache/samply/blaze:0.31
|
||||
image: docker.verbis.dkfz.de/cache/samply/blaze:${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"
|
||||
|
@ -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: ${FOCUS_ENDPOINT_TYPE:-blaze}
|
||||
volumes:
|
||||
- /srv/docker/bridgehead/itcc/queries_to_cache.conf:/queries_to_cache.conf:ro
|
||||
depends_on:
|
||||
- "beam-proxy"
|
||||
- "blaze"
|
||||
|
2
itcc/queries_to_cache.conf
Normal file
2
itcc/queries_to_cache.conf
Normal file
@ -0,0 +1,2 @@
|
||||
bGlicmFyeSBSZXRyaWV2ZQp1c2luZyBGSElSIHZlcnNpb24gJzQuMC4wJwppbmNsdWRlIEZISVJIZWxwZXJzIHZlcnNpb24gJzQuMC4wJwpjb2Rlc3lzdGVtIFNhbXBsZU1hdGVyaWFsVHlwZTogJ2h0dHBzOi8vZmhpci5iYm1yaS5kZS9Db2RlU3lzdGVtL1NhbXBsZU1hdGVyaWFsVHlwZScKCmNvZGVzeXN0ZW0gbG9pbmM6ICdodHRwOi8vbG9pbmMub3JnJwoKY29udGV4dCBQYXRpZW50CkRLVEtfU1RSQVRfR0VOREVSX1NUUkFUSUZJRVIKICBES1RLX1NUUkFUX0RJQUdOT1NJU19TVFJBVElGSUVSCiAgSVRDQ19TVFJBVF9BR0VfQ0xBU1NfU1RSQVRJRklFUgogIERLVEtfU1RSQVRfREVGX0lOX0lOSVRJQUxfUE9QVUxBVElPTgp0cnVl
|
||||
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
|
@ -6,7 +6,7 @@ services:
|
||||
replicas: 0 #deactivate landing page
|
||||
|
||||
blaze:
|
||||
image: docker.verbis.dkfz.de/cache/samply/blaze:0.31
|
||||
image: docker.verbis.dkfz.de/cache/samply/blaze:${BLAZE_TAG}
|
||||
container_name: bridgehead-kr-blaze
|
||||
environment:
|
||||
BASE_URL: "http://bridgehead-kr-blaze:8080"
|
||||
|
@ -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: "${ENABLE_DATASHIELD}"
|
||||
|
@ -3,7 +3,5 @@
|
||||
if [ "$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
|
||||
|
@ -116,7 +116,7 @@ assertVarsNotEmpty() {
|
||||
MISSING_VARS=""
|
||||
|
||||
for VAR in $@; do
|
||||
if [ -z "${!VAR}" ]; then
|
||||
if [ -z "${!VAR}" ]; then
|
||||
MISSING_VARS+="$VAR "
|
||||
fi
|
||||
done
|
||||
@ -313,15 +313,82 @@ 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
|
||||
|
||||
set -a # Export variables as environment variables
|
||||
source /var/cache/bridgehead/secrets/*
|
||||
source /var/cache/bridgehead/secrets/oidc
|
||||
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}"
|
||||
|
11
lib/gitlab-token-helper.sh
Executable file
11
lib/gitlab-token-helper.sh
Executable file
@ -0,0 +1,11 @@
|
||||
#!/bin/bash
|
||||
|
||||
[ "$1" = "get" ] || exit
|
||||
|
||||
source "/tmp/bridgehead/secret-sync.boot-$(cat /proc/sys/kernel/random/boot_id)/gitlab-token"
|
||||
|
||||
# Any non-empty username works, only the token matters
|
||||
cat << EOF
|
||||
username=bk
|
||||
password=$BRIDGEHEAD_CONFIG_REPO_TOKEN
|
||||
EOF
|
@ -1,41 +0,0 @@
|
||||
#!/bin/bash
|
||||
|
||||
if [ "$1" != "get" ]; then
|
||||
echo "Usage: $0 get"
|
||||
exit 1
|
||||
fi
|
||||
|
||||
baseDir() {
|
||||
# see https://stackoverflow.com/questions/59895
|
||||
SOURCE=${BASH_SOURCE[0]}
|
||||
while [ -h "$SOURCE" ]; do # resolve $SOURCE until the file is no longer a symlink
|
||||
DIR=$( cd -P "$( dirname "$SOURCE" )" >/dev/null 2>&1 && pwd )
|
||||
SOURCE=$(readlink "$SOURCE")
|
||||
[[ $SOURCE != /* ]] && SOURCE=$DIR/$SOURCE # if $SOURCE was a relative symlink, we need to resolve it relative to the path where the symlink file was located
|
||||
done
|
||||
DIR=$( cd -P "$( dirname "$SOURCE" )/.." >/dev/null 2>&1 && pwd )
|
||||
echo $DIR
|
||||
}
|
||||
|
||||
BASE=$(baseDir)
|
||||
cd $BASE
|
||||
|
||||
source lib/functions.sh
|
||||
|
||||
assertVarsNotEmpty SITE_ID || fail_and_report 1 "gitpassword.sh failed: SITE_ID is empty."
|
||||
|
||||
PARAMS="$(cat)"
|
||||
GITHOST=$(echo "$PARAMS" | grep "^host=" | sed 's/host=\(.*\)/\1/g')
|
||||
|
||||
fetchVarsFromVault GIT_PASSWORD
|
||||
|
||||
if [ -z "${GIT_PASSWORD}" ]; then
|
||||
fail_and_report 1 "gitpassword.sh failed: Git password not found."
|
||||
fi
|
||||
|
||||
cat <<EOF
|
||||
protocol=https
|
||||
host=$GITHOST
|
||||
username=bk-${SITE_ID}
|
||||
password=${GIT_PASSWORD}
|
||||
EOF
|
@ -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 \
|
||||
|
@ -19,7 +19,7 @@ fi
|
||||
|
||||
hc_send log "Checking for bridgehead updates ..."
|
||||
|
||||
CONFFILE=/etc/bridgehead/$1.conf
|
||||
CONFFILE=/etc/bridgehead/$PROJECT.conf
|
||||
|
||||
if [ ! -e $CONFFILE ]; then
|
||||
fail_and_report 1 "Configuration file $CONFFILE not found."
|
||||
@ -33,7 +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"
|
||||
|
||||
CREDHELPER="/srv/docker/bridgehead/lib/gitpassword.sh"
|
||||
secret_sync_gitlab_token
|
||||
|
||||
CHANGES=""
|
||||
|
||||
@ -45,10 +45,6 @@ for DIR in /etc/bridgehead $(pwd); do
|
||||
if [ -n "$OUT" ]; then
|
||||
report_error log "The working directory $DIR is modified. Changed files: $OUT"
|
||||
fi
|
||||
if [ "$(git -C $DIR config --get credential.helper)" != "$CREDHELPER" ]; then
|
||||
log "INFO" "Configuring repo to use bridgehead git credential helper."
|
||||
git -C $DIR config credential.helper "$CREDHELPER"
|
||||
fi
|
||||
old_git_hash="$(git -C $DIR rev-parse --verify HEAD)"
|
||||
if [ -z "$HTTPS_PROXY_FULL_URL" ]; then
|
||||
log "INFO" "Git is using no proxy!"
|
||||
|
@ -16,7 +16,7 @@ services:
|
||||
- --entrypoints.web.http.redirections.entrypoint.scheme=https
|
||||
labels:
|
||||
- "traefik.enable=true"
|
||||
- "traefik.http.routers.dashboard.rule=PathPrefix(`/api`) || PathPrefix(`/dashboard/`)"
|
||||
- "traefik.http.routers.dashboard.rule=PathPrefix(`/dashboard/`)"
|
||||
- "traefik.http.routers.dashboard.entrypoints=websecure"
|
||||
- "traefik.http.routers.dashboard.service=api@internal"
|
||||
- "traefik.http.routers.dashboard.tls=true"
|
||||
|
142
minimal/modules/dnpm-central-targets.json
Normal file
142
minimal/modules/dnpm-central-targets.json
Normal file
@ -0,0 +1,142 @@
|
||||
{
|
||||
"sites": [
|
||||
{
|
||||
"id": "UKFR",
|
||||
"name": "Freiburg",
|
||||
"virtualhost": "ukfr.dnpm.de",
|
||||
"beamconnect": "dnpm-connect.dnpm-bridge.broker.ccp-it.dktk.dkfz.de"
|
||||
},
|
||||
{
|
||||
"id": "UKHD",
|
||||
"name": "Heidelberg",
|
||||
"virtualhost": "ukhd.dnpm.de",
|
||||
"beamconnect": "dnpm-connect.dnpm-bridge.broker.ccp-it.dktk.dkfz.de"
|
||||
},
|
||||
{
|
||||
"id": "UKT",
|
||||
"name": "Tübingen",
|
||||
"virtualhost": "ukt.dnpm.de",
|
||||
"beamconnect": "dnpm-connect.dnpm-bridge.broker.ccp-it.dktk.dkfz.de"
|
||||
},
|
||||
{
|
||||
"id": "UKU",
|
||||
"name": "Ulm",
|
||||
"virtualhost": "uku.dnpm.de",
|
||||
"beamconnect": "dnpm-connect.dnpm-bridge.broker.ccp-it.dktk.dkfz.de"
|
||||
},
|
||||
{
|
||||
"id": "UM",
|
||||
"name": "Mainz",
|
||||
"virtualhost": "um.dnpm.de",
|
||||
"beamconnect": "dnpm-connect.dnpm-bridge.broker.ccp-it.dktk.dkfz.de"
|
||||
},
|
||||
{
|
||||
"id": "UKMR",
|
||||
"name": "Marburg",
|
||||
"virtualhost": "ukmr.dnpm.de",
|
||||
"beamconnect": "dnpm-connect.dnpm-bridge.broker.ccp-it.dktk.dkfz.de"
|
||||
},
|
||||
{
|
||||
"id": "UKE",
|
||||
"name": "Hamburg",
|
||||
"virtualhost": "uke.dnpm.de",
|
||||
"beamconnect": "dnpm-connect.dnpm-bridge.broker.ccp-it.dktk.dkfz.de"
|
||||
},
|
||||
{
|
||||
"id": "UKA",
|
||||
"name": "Aachen",
|
||||
"virtualhost": "uka.dnpm.de",
|
||||
"beamconnect": "dnpm-connect.dnpm-bridge.broker.ccp-it.dktk.dkfz.de"
|
||||
},
|
||||
{
|
||||
"id": "Charite",
|
||||
"name": "Berlin",
|
||||
"virtualhost": "charite.dnpm.de",
|
||||
"beamconnect": "dnpm-connect.berlin-test.broker.ccp-it.dktk.dkfz.de"
|
||||
},
|
||||
{
|
||||
"id": "MRI",
|
||||
"name": "Muenchen-tum",
|
||||
"virtualhost": "mri.dnpm.de",
|
||||
"beamconnect": "dnpm-connect.muenchen-tum.broker.ccp-it.dktk.dkfz.de"
|
||||
},
|
||||
{
|
||||
"id": "KUM",
|
||||
"name": "Muenchen-lmu",
|
||||
"virtualhost": "kum.dnpm.de",
|
||||
"beamconnect": "dnpm-connect.muenchen-lmu.broker.ccp-it.dktk.dkfz.de"
|
||||
},
|
||||
{
|
||||
"id": "MHH",
|
||||
"name": "Hannover",
|
||||
"virtualhost": "mhh.dnpm.de",
|
||||
"beamconnect": "dnpm-connect.hannover.broker.ccp-it.dktk.dkfz.de"
|
||||
},
|
||||
{
|
||||
"id": "UKDD",
|
||||
"name": "dresden-dnpm",
|
||||
"virtualhost": "ukdd.dnpm.de",
|
||||
"beamconnect": "dnpm-connect.dresden-dnpm.broker.ccp-it.dktk.dkfz.de"
|
||||
},
|
||||
{
|
||||
"id": "UKB",
|
||||
"name": "Bonn",
|
||||
"virtualhost": "ukb.dnpm.de",
|
||||
"beamconnect": "dnpm-connect.bonn-dnpm.broker.ccp-it.dktk.dkfz.de"
|
||||
},
|
||||
{
|
||||
"id": "UKD",
|
||||
"name": "Duesseldorf",
|
||||
"virtualhost": "ukd.dnpm.de",
|
||||
"beamconnect": "dnpm-connect.duesseldorf-dnpm.broker.ccp-it.dktk.dkfz.de"
|
||||
},
|
||||
{
|
||||
"id": "UKK",
|
||||
"name": "Koeln",
|
||||
"virtualhost": "ukk.dnpm.de",
|
||||
"beamconnect": "dnpm-connect.dnpm-bridge.broker.ccp-it.dktk.dkfz.de"
|
||||
},
|
||||
{
|
||||
"id": "UME",
|
||||
"name": "Essen",
|
||||
"virtualhost": "ume.dnpm.de",
|
||||
"beamconnect": "dnpm-connect.essen.broker.ccp-it.dktk.dkfz.de"
|
||||
},
|
||||
{
|
||||
"id": "UKM",
|
||||
"name": "Muenster",
|
||||
"virtualhost": "ukm.dnpm.de",
|
||||
"beamconnect": "dnpm-connect.muenster-dnpm.broker.ccp-it.dktk.dkfz.de"
|
||||
},
|
||||
{
|
||||
"id": "UKF",
|
||||
"name": "Frankfurt",
|
||||
"virtualhost": "ukf.dnpm.de",
|
||||
"beamconnect": "dnpm-connect.frankfurt.broker.ccp-it.dktk.dkfz.de"
|
||||
},
|
||||
{
|
||||
"id": "UMG",
|
||||
"name": "Goettingen",
|
||||
"virtualhost": "umg.dnpm.de",
|
||||
"beamconnect": "dnpm-connect.goettingen.broker.ccp-it.dktk.dkfz.de"
|
||||
},
|
||||
{
|
||||
"id": "UKW",
|
||||
"name": "Würzburg",
|
||||
"virtualhost": "ukw.dnpm.de",
|
||||
"beamconnect": "dnpm-connect.wuerzburg-dnpm.broker.ccp-it.dktk.dkfz.de"
|
||||
},
|
||||
{
|
||||
"id": "UKSH",
|
||||
"name": "Schleswig-Holstein",
|
||||
"virtualhost": "uksh.dnpm.de",
|
||||
"beamconnect": "dnpm-connect.uksh-dnpm.broker.ccp-it.dktk.dkfz.de"
|
||||
},
|
||||
{
|
||||
"id": "TKT",
|
||||
"name": "Test",
|
||||
"virtualhost": "tkt.dnpm.de",
|
||||
"beamconnect": "dnpm-connect.tobias-develop.broker.ccp-it.dktk.dkfz.de"
|
||||
}
|
||||
]
|
||||
}
|
@ -29,7 +29,7 @@ services:
|
||||
PROXY_APIKEY: ${DNPM_BEAM_SECRET_SHORT}
|
||||
APP_ID: dnpm-connect.${DNPM_PROXY_ID}
|
||||
DISCOVERY_URL: "./conf/central_targets.json"
|
||||
LOCAL_TARGETS_FILE: "./conf/connect_targets.json"
|
||||
LOCAL_TARGETS_FILE: "/conf/connect_targets.json"
|
||||
HTTP_PROXY: http://forward_proxy:3128
|
||||
HTTPS_PROXY: http://forward_proxy:3128
|
||||
NO_PROXY: dnpm-beam-proxy,dnpm-backend, host.docker.internal${DNPM_ADDITIONAL_NO_PROXY}
|
||||
@ -41,7 +41,7 @@ services:
|
||||
volumes:
|
||||
- /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro
|
||||
- /etc/bridgehead/dnpm/local_targets.json:/conf/connect_targets.json:ro
|
||||
- /etc/bridgehead/dnpm/central_targets.json:/conf/central_targets.json:ro
|
||||
- /srv/docker/bridgehead/minimal/modules/dnpm-central-targets.json:/conf/central_targets.json:ro
|
||||
labels:
|
||||
- "traefik.enable=true"
|
||||
- "traefik.http.routers.dnpm-connect.rule=PathPrefix(`/dnpm-connect`)"
|
||||
|
@ -1,34 +1,99 @@
|
||||
version: "3.7"
|
||||
|
||||
services:
|
||||
dnpm-backend:
|
||||
image: ghcr.io/kohlbacherlab/bwhc-backend:1.0-snapshot-broker-connector
|
||||
container_name: bridgehead-dnpm-backend
|
||||
dnpm-mysql:
|
||||
image: mysql:9
|
||||
healthcheck:
|
||||
test: [ "CMD", "mysqladmin" ,"ping", "-h", "localhost" ]
|
||||
interval: 3s
|
||||
timeout: 5s
|
||||
retries: 5
|
||||
environment:
|
||||
- ZPM_SITE=${ZPM_SITE}
|
||||
- N_RANDOM_FILES=${DNPM_SYNTH_NUM}
|
||||
MYSQL_ROOT_HOST: "%"
|
||||
MYSQL_ROOT_PASSWORD: ${DNPM_MYSQL_ROOT_PASSWORD}
|
||||
volumes:
|
||||
- /etc/bridgehead/dnpm:/bwhc_config:ro
|
||||
- ${DNPM_DATA_DIR}:/bwhc_data
|
||||
labels:
|
||||
- "traefik.enable=true"
|
||||
- "traefik.http.routers.bwhc-backend.rule=PathPrefix(`/bwhc`)"
|
||||
- "traefik.http.services.bwhc-backend.loadbalancer.server.port=9000"
|
||||
- "traefik.http.routers.bwhc-backend.tls=true"
|
||||
- /var/cache/bridgehead/dnpm/mysql:/var/lib/mysql
|
||||
|
||||
dnpm-frontend:
|
||||
image: ghcr.io/kohlbacherlab/bwhc-frontend:2209
|
||||
container_name: bridgehead-dnpm-frontend
|
||||
links:
|
||||
- dnpm-backend
|
||||
dnpm-authup:
|
||||
image: authup/authup:latest
|
||||
container_name: bridgehead-dnpm-authup
|
||||
volumes:
|
||||
- /var/cache/bridgehead/dnpm/authup:/usr/src/app/writable
|
||||
depends_on:
|
||||
dnpm-mysql:
|
||||
condition: service_healthy
|
||||
command: server/core start
|
||||
environment:
|
||||
- NUXT_HOST=0.0.0.0
|
||||
- NUXT_PORT=8080
|
||||
- BACKEND_PROTOCOL=https
|
||||
- BACKEND_HOSTNAME=$HOST
|
||||
- BACKEND_PORT=443
|
||||
- PUBLIC_URL=https://${HOST}/auth/
|
||||
- AUTHORIZE_REDIRECT_URL=https://${HOST}
|
||||
- ROBOT_ADMIN_ENABLED=true
|
||||
- ROBOT_ADMIN_SECRET=${DNPM_AUTHUP_SECRET}
|
||||
- ROBOT_ADMIN_SECRET_RESET=true
|
||||
- DB_TYPE=mysql
|
||||
- DB_HOST=dnpm-mysql
|
||||
- DB_USERNAME=root
|
||||
- DB_PASSWORD=${DNPM_MYSQL_ROOT_PASSWORD}
|
||||
- DB_DATABASE=auth
|
||||
labels:
|
||||
- "traefik.enable=true"
|
||||
- "traefik.http.routers.bwhc-frontend.rule=PathPrefix(`/`)"
|
||||
- "traefik.http.services.bwhc-frontend.loadbalancer.server.port=8080"
|
||||
- "traefik.http.routers.bwhc-frontend.tls=true"
|
||||
- "traefik.http.middlewares.authup-strip.stripprefix.prefixes=/auth/"
|
||||
- "traefik.http.routers.dnpm-auth.middlewares=authup-strip"
|
||||
- "traefik.http.routers.dnpm-auth.rule=PathPrefix(`/auth`)"
|
||||
- "traefik.http.services.dnpm-auth.loadbalancer.server.port=3000"
|
||||
- "traefik.http.routers.dnpm-auth.tls=true"
|
||||
|
||||
dnpm-portal:
|
||||
image: ghcr.io/dnpm-dip/portal:latest
|
||||
container_name: bridgehead-dnpm-portal
|
||||
environment:
|
||||
- NUXT_API_URL=http://dnpm-backend:9000/
|
||||
- NUXT_PUBLIC_API_URL=https://${HOST}/api/
|
||||
- NUXT_AUTHUP_URL=http://dnpm-authup:3000/
|
||||
- NUXT_PUBLIC_AUTHUP_URL=https://${HOST}/auth/
|
||||
labels:
|
||||
- "traefik.enable=true"
|
||||
- "traefik.http.routers.dnpm-frontend.rule=PathPrefix(`/`)"
|
||||
- "traefik.http.services.dnpm-frontend.loadbalancer.server.port=3000"
|
||||
- "traefik.http.routers.dnpm-frontend.tls=true"
|
||||
|
||||
dnpm-backend:
|
||||
container_name: bridgehead-dnpm-backend
|
||||
image: ghcr.io/dnpm-dip/backend:latest
|
||||
environment:
|
||||
- LOCAL_SITE=${ZPM_SITE}:${SITE_NAME} # Format: {Site-ID}:{Site-name}, e.g. UKT:Tübingen
|
||||
- RD_RANDOM_DATA=${DNPM_SYNTH_NUM:--1}
|
||||
- MTB_RANDOM_DATA=${DNPM_SYNTH_NUM:--1}
|
||||
- HATEOAS_HOST=https://${HOST}
|
||||
- CONNECTOR_TYPE=broker
|
||||
- AUTHUP_URL=robot://system:${DNPM_AUTHUP_SECRET}@http://dnpm-authup:3000
|
||||
volumes:
|
||||
- /etc/bridgehead/dnpm/config:/dnpm_config
|
||||
- /var/cache/bridgehead/dnpm/backend-data:/dnpm_data
|
||||
depends_on:
|
||||
dnpm-authup:
|
||||
condition: service_healthy
|
||||
labels:
|
||||
- "traefik.enable=true"
|
||||
- "traefik.http.services.dnpm-backend.loadbalancer.server.port=9000"
|
||||
# expose everything
|
||||
- "traefik.http.routers.dnpm-backend.rule=PathPrefix(`/api`)"
|
||||
- "traefik.http.routers.dnpm-backend.tls=true"
|
||||
- "traefik.http.routers.dnpm-backend.service=dnpm-backend"
|
||||
# except ETL
|
||||
- "traefik.http.routers.dnpm-backend-etl.rule=PathRegexp(`^/api(/.*)?etl(/.*)?$`)"
|
||||
- "traefik.http.routers.dnpm-backend-etl.tls=true"
|
||||
- "traefik.http.routers.dnpm-backend-etl.service=dnpm-backend"
|
||||
# this needs an ETL processor with support for basic auth
|
||||
- "traefik.http.routers.dnpm-backend-etl.middlewares=auth"
|
||||
# except peer-to-peer
|
||||
- "traefik.http.routers.dnpm-backend-peer.rule=PathRegexp(`^/api(/.*)?/peer2peer(/.*)?$`)"
|
||||
- "traefik.http.routers.dnpm-backend-peer.tls=true"
|
||||
- "traefik.http.routers.dnpm-backend-peer.service=dnpm-backend"
|
||||
- "traefik.http.routers.dnpm-backend-peer.middlewares=dnpm-backend-peer"
|
||||
# this effectively denies all requests
|
||||
# this is okay, because requests from peers don't go through Traefik
|
||||
- "traefik.http.middlewares.dnpm-backend-peer.ipWhiteList.sourceRange=0.0.0.0/32"
|
||||
|
||||
landing:
|
||||
labels:
|
||||
- "traefik.http.routers.landing.rule=PathPrefix(`/landing`)"
|
||||
|
@ -1,28 +1,16 @@
|
||||
#!/bin/bash
|
||||
|
||||
if [ -n "${ENABLE_DNPM_NODE}" ]; then
|
||||
log INFO "DNPM setup detected (BwHC Node) -- will start BwHC node."
|
||||
log INFO "DNPM setup detected -- will start DNPM:DIP node."
|
||||
OVERRIDE+=" -f ./$PROJECT/modules/dnpm-node-compose.yml"
|
||||
|
||||
# Set variables required for BwHC Node. ZPM_SITE is assumed to be set in /etc/bridgehead/<project>.conf
|
||||
DNPM_APPLICATION_SECRET="$(echo \"This is a salt string to generate one consistent password for DNPM. It is not required to be secret.\" | sha1sum | openssl pkeyutl -sign -inkey /etc/bridgehead/pki/${SITE_ID}.priv.pem | base64 | head -c 30)"
|
||||
if [ -z "${ZPM_SITE+x}" ]; then
|
||||
log ERROR "Mandatory variable ZPM_SITE not defined!"
|
||||
exit 1
|
||||
fi
|
||||
if [ -z "${DNPM_DATA_DIR+x}" ]; then
|
||||
log ERROR "Mandatory variable DNPM_DATA_DIR not defined!"
|
||||
exit 1
|
||||
fi
|
||||
DNPM_SYNTH_NUM=${DNPM_SYNTH_NUM:-0}
|
||||
if grep -q 'traefik.http.routers.landing.rule=PathPrefix(`/landing`)' /srv/docker/bridgehead/minimal/docker-compose.override.yml 2>/dev/null; then
|
||||
echo "Override of landing page url already in place"
|
||||
else
|
||||
echo "Adding override of landing page url"
|
||||
if [ -f /srv/docker/bridgehead/minimal/docker-compose.override.yml ]; then
|
||||
echo -e ' landing:\n labels:\n - "traefik.http.routers.landing.rule=PathPrefix(`/landing`)"' >> /srv/docker/bridgehead/minimal/docker-compose.override.yml
|
||||
else
|
||||
echo -e 'version: "3.7"\nservices:\n landing:\n labels:\n - "traefik.http.routers.landing.rule=PathPrefix(`/landing`)"' >> /srv/docker/bridgehead/minimal/docker-compose.override.yml
|
||||
fi
|
||||
fi
|
||||
mkdir -p /var/cache/bridgehead/dnpm/ || fail_and_report 1 "Failed to create '/var/cache/bridgehead/dnpm/'. Please run sudo './bridgehead install $PROJECT' again to fix the permissions."
|
||||
DNPM_SYNTH_NUM=${DNPM_SYNTH_NUM:--1}
|
||||
DNPM_MYSQL_ROOT_PASSWORD="$(generate_simple_password 'dnpm mysql')"
|
||||
DNPM_AUTHUP_SECRET="$(generate_simple_password 'dnpm authup')"
|
||||
fi
|
||||
|
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 ./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 +5,13 @@ services:
|
||||
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
|
||||
- INSTITUTE_TTP_URL
|
||||
- INSTITUTE_TTP_API_KEY
|
||||
- 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}
|
||||
@ -17,11 +22,27 @@ services:
|
||||
- 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:0.28
|
||||
image: docker.verbis.dkfz.de/cache/samply/blaze:${BLAZE_TAG}
|
||||
container_name: bridgehead-transfair-input-blaze
|
||||
environment:
|
||||
BASE_URL: "http://bridgehead-transfair-input-blaze:8080"
|
||||
@ -32,12 +53,19 @@ services:
|
||||
volumes:
|
||||
- "transfair-input-blaze-data:/app/data"
|
||||
profiles: ["transfair-input-blaze"]
|
||||
labels:
|
||||
- "traefik.enable=true"
|
||||
- "traefik.http.routers.transfair-input-blaze.rule=PathPrefix(`/data-delivery`)"
|
||||
- "traefik.http.middlewares.transfair-input-strip.stripprefix.prefixes=/data-delivery"
|
||||
- "traefik.http.services.transfair-input-blaze.loadbalancer.server.port=8080"
|
||||
- "traefik.http.routers.transfair-input-blaze.middlewares=transfair-input-strip,transfair-auth"
|
||||
- "traefik.http.routers.transfair-input-blaze.tls=true"
|
||||
|
||||
transfair-request-blaze:
|
||||
image: docker.verbis.dkfz.de/cache/samply/blaze:0.28
|
||||
container_name: bridgehead-transfair-requests-blaze
|
||||
image: docker.verbis.dkfz.de/cache/samply/blaze:${BLAZE_TAG}
|
||||
container_name: bridgehead-transfair-request-blaze
|
||||
environment:
|
||||
BASE_URL: "http://bridgehead-transfair-requests-blaze:8080"
|
||||
BASE_URL: "http://bridgehead-transfair-request-blaze:8080"
|
||||
JAVA_TOOL_OPTIONS: "-Xmx1024m"
|
||||
DB_BLOCK_CACHE_SIZE: 1024
|
||||
CQL_EXPR_CACHE_SIZE: 8
|
||||
@ -45,6 +73,13 @@ services:
|
||||
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:
|
||||
|
@ -1,7 +1,7 @@
|
||||
#!/bin/bash -e
|
||||
|
||||
function transfairSetup() {
|
||||
if [[ -n "$INSTITUTE_TTP_URL" || -n "$EXCHANGE_ID_SYSTEM" ]]; then
|
||||
if [[ -n "$TTP_URL" || -n "$EXCHANGE_ID_SYSTEM" ]]; then
|
||||
echo "Starting transfair."
|
||||
OVERRIDE+=" -f ./modules/transfair-compose.yml"
|
||||
if [ -n "$FHIR_INPUT_URL" ]; then
|
||||
@ -15,8 +15,21 @@ function transfairSetup() {
|
||||
log INFO "TransFAIR request fhir store set to external $FHIR_REQUEST_URL"
|
||||
else
|
||||
log INFO "TransFAIR request fhir store not set writing to internal blaze"
|
||||
FHIR_REQUEST_URL="http://transfair-requests-blaze:8080"
|
||||
FHIR_REQUEST_URL="http://transfair-request-blaze:8080"
|
||||
OVERRIDE+=" --profile transfair-request-blaze"
|
||||
fi
|
||||
if [ -n "$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
3
versions/acceptance
Normal file
@ -0,0 +1,3 @@
|
||||
FOCUS_TAG=develop
|
||||
BEAM_TAG=develop
|
||||
BLAZE_TAG=main
|
3
versions/prod
Normal file
3
versions/prod
Normal file
@ -0,0 +1,3 @@
|
||||
FOCUS_TAG=main
|
||||
BEAM_TAG=main
|
||||
BLAZE_TAG=0.32
|
3
versions/test
Normal file
3
versions/test
Normal file
@ -0,0 +1,3 @@
|
||||
FOCUS_TAG=develop
|
||||
BEAM_TAG=develop
|
||||
BLAZE_TAG=main
|
Reference in New Issue
Block a user