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16 Commits

Author SHA1 Message Date
Martin Jurk
9c022ffb88 refactor and clean up 2025-12-04 15:47:12 +01:00
Martin Jurk
6525bb45e4 refactor 2025-12-04 11:36:15 +01:00
martin.jurk
c8ed52e73e endpoint with api key 2025-12-03 13:53:12 +01:00
Martin Jurk
371ed7f26e trafic error fixed 2025-12-01 16:41:45 +01:00
Martin Jurk
6ffa4260b9 volume changed /srv/docker/data 2025-12-01 13:31:52 +01:00
martin.jurk
cdbc25270a missing Sites env error 2025-11-25 15:48:02 +01:00
Martin Jurk
02a3a87ebd script to optional use omics 2025-11-25 08:35:09 +01:00
Martin Jurk
b8bef62ed7 wrong focus id 2025-11-24 15:28:24 +01:00
Martin Jurk
919e705d35 omic test env 2025-11-24 15:12:01 +01:00
Martin Jurk
e4cfd41874 explorer error host fix 2025-11-21 10:26:28 +01:00
Martin Jurk
bd648b027b test lens2 migration 2025-11-12 15:16:17 +01:00
Niklas Reimer
ab6e05826f feat(dnpm): set timezone to Europe/Berlin (#359) 2025-11-12 10:25:20 +01:00
DavidCroftDKFZ
394dcc2567 Directory sync: token login and cron change (#351)
The Directory team have requested that we allow token login to the
Directory, where a user uses LSAAI credentials to obtain a token from
the Directory, and then uses this to authenticate Directory sync. This
has been implemented via an environment variable, in an analogous way to
the already existing username/password method.

The default start time for the Directory sync has been shifted to 22:30,
to prevent conflicts with the Bridgehead auto-update.

Relevant changes have been made to the documentation.

Co-authored-by: Torben Brenner <76154651+torbrenner@users.noreply.github.com>
Co-authored-by: Jan <59206115+Threated@users.noreply.github.com>
Co-authored-by: Martin Lablans <6804500+lablans@users.noreply.github.com>
2025-11-11 09:43:08 +01:00
djuarezgf
58d3e6487c feat: add nNGM project (#340) 2025-11-06 16:47:50 +01:00
Pierre Delpy
230ff1debb feat: add PSCC
* add pscc and prepare lens2 deployment
---------

Co-authored-by: p.delpy@dkfz-heidelberg.de <p.delpy@dkfz-heidelberg.de>
Co-authored-by: Jan <59206115+Threated@users.noreply.github.com>
2025-11-05 15:18:00 +01:00
DavidCroftDKFZ
6dea7c8fef Directory sync: inherit host timezone (#354)
Directory sync needs to be able to launch at specific times of day, and in order to do this in a predictable way, the timezone used inside the Docker container should be the same as the host. To do this, two files need to be mounted from the host. One file contains information about the time zone, the other file contains the file zone name.
2025-11-05 11:02:26 +01:00
30 changed files with 528 additions and 90 deletions

View File

@@ -318,6 +318,12 @@ To enable it, you will need to explicitly set the username and password variable
DS_DIRECTORY_USER_NAME=your_directory_username
DS_DIRECTORY_USER_PASS=your_directory_password
```
Alternatively, if you have obtained a token from the Directory, you can insert the following into the configuration file:
```
DS_DIRECTORY_USER_TOKEN=your_directory_token
```
If you don't supply any authentification information (either login credentials or a token), Directory sync will not start.
Please contact your National Node or Directory support (directory-dev@helpdesk.bbmri-eric.eu) to obtain these credentials.
The following environment variables can be used from within your config file to control the behavior of Directory sync:
@@ -325,12 +331,13 @@ The following environment variables can be used from within your config file to
| Variable | Purpose | Default if not specified |
|:-----------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------|
| DS_DIRECTORY_URL | Base URL of the Directory | https://directory-backend.molgenis.net |
| DS_DIRECTORY_USER_NAME | User name for logging in to Directory **Mandatory** | |
| DS_DIRECTORY_USER_PASS | Password for logging in to Directory **Mandatory** | |
| DS_DIRECTORY_USER_NAME | User name for logging in to Directory | |
| DS_DIRECTORY_USER_PASS | Password for logging in to Directory | |
| DS_DIRECTORY_USER_TOKEN | Token for logging in to Directory | |
| DS_DIRECTORY_DEFAULT_COLLECTION_ID | ID of collection to be used if not in samples | |
| DS_DIRECTORY_ALLOW_STAR_MODEL | Set to 'True' to send star model info to Directory | True |
| DS_FHIR_STORE_URL | URL for FHIR store | http://bridgehead-bbmri-blaze:8080 |
| DS_TIMER_CRON | Execution interval for Directory sync, [cron](https://crontab.guru) format | 0 22 * * * |
| DS_TIMER_CRON | Execution interval for Directory sync, [cron](https://crontab.guru) format | 30 22 * * * |
| DS_IMPORT_BIOBANKS | Set to 'True' to import biobank metadata from Directory | True |
| DS_IMPORT_COLLECTIONS | Set to 'True' to import collection metadata from Directory | True |

View File

@@ -7,7 +7,8 @@ services:
DS_DIRECTORY_URL: ${DS_DIRECTORY_URL:-https://directory.bbmri-eric.eu}
DS_DIRECTORY_USER_NAME: ${DS_DIRECTORY_USER_NAME}
DS_DIRECTORY_USER_PASS: ${DS_DIRECTORY_USER_PASS}
DS_TIMER_CRON: ${DS_TIMER_CRON:-0 22 * * *}
DS_DIRECTORY_USER_TOKEN: ${DS_DIRECTORY_USER_TOKEN}
DS_TIMER_CRON: ${DS_TIMER_CRON:-30 22 * * *}
DS_DIRECTORY_ALLOW_STAR_MODEL: ${DS_DIRECTORY_ALLOW_STAR_MODEL:-true}
DS_DIRECTORY_MOCK: ${DS_DIRECTORY_MOCK}
DS_DIRECTORY_DEFAULT_COLLECTION_ID: ${DS_DIRECTORY_DEFAULT_COLLECTION_ID}
@@ -16,3 +17,6 @@ services:
DS_IMPORT_COLLECTIONS: ${DS_IMPORT_COLLECTIONS:-true}
depends_on:
- "blaze"
volumes:
- /etc/localtime:/etc/localtime:ro # inherit host timezone
- /etc/timezone:/etc/timezone:ro # inherit host timezone name

View File

@@ -35,6 +35,9 @@ case "$PROJECT" in
cce)
#nothing extra to do
;;
pscc)
#nothing extra to do
;;
itcc)
#nothing extra to do
;;
@@ -44,6 +47,9 @@ case "$PROJECT" in
dhki)
#nothing extra to do
;;
nngm)
#nothing extra to do
;;
minimal)
#nothing extra to do
;;
@@ -180,13 +186,6 @@ case "$ACTION" in
;;
postRun | postUpdate)
;;
send-file)
loadVars
log "WARNING" "Your are about to send a file to another bridgehead in your network!"
read -p "Please name the bridgehead you want to send the file to (proxy-id): " RECEIVER_PROXY_ID
read -p "Continue? (Y/N): " confirm && [[ $confirm == [yY] || $confirm == [yY][eE][sS] ]] || exit 1
exec $COMPOSE -p $PROJECT -f ./modules/beam-file-compose.yml --profile beam-file-sender run beam-file-sender send --to beamfile.$RECEIVER_PROXY_ID /data/outfile
;;
*)
printUsage
exit 1

View File

@@ -1,32 +1,39 @@
version: "3.7"
services:
landing:
lens:
container_name: lens_federated-search
image: docker.verbis.dkfz.de/ccp/lens:${SITE_ID}
image: ghcr.io/samply/cce-explorer:pr-1
labels:
- "traefik.http.services.lens.loadbalancer.server.port=3000"
- "traefik.enable=true"
- "traefik.http.routers.landing.rule=PathPrefix(`/`)"
- "traefik.http.services.landing.loadbalancer.server.port=80"
- "traefik.http.routers.landing.tls=true"
- "traefik.http.routers.lens.rule=Host(`${HOST}`)"
- "traefik.http.routers.lens.tls=true"
spot:
image: docker.verbis.dkfz.de/ccp-private/central-spot
image: samply/rustyspot:latest
environment:
HTTP_PROXY: ${HTTP_PROXY_URL}
HTTPS_PROXY: ${HTTPS_PROXY_URL}
NO_PROXY: beam-proxy
BEAM_SECRET: "${FOCUS_BEAM_SECRET_SHORT}"
BEAM_URL: http://beam-proxy:8081
BEAM_PROXY_ID: ${SITE_ID}
BEAM_BROKER_ID: ${BROKER_ID}
BEAM_APP_ID: "focus"
BEAM_PROXY_URL: http://beam-proxy:8081
BEAM_APP_ID: "spot.${SITE_ID}.${BROKER_ID}"
CORS_ORIGIN: "https://${HOST}"
SITES: ${SITES}
TRANSFORM: LENS
PROJECT: cce
BIND_ADDR: 0.0.0.0:8055
depends_on:
- "beam-proxy"
labels:
- "traefik.enable=true"
- "traefik.http.services.spot.loadbalancer.server.port=8080"
- "traefik.http.services.spot.loadbalancer.server.port=8055"
- "traefik.http.middlewares.corsheaders2.headers.accesscontrolallowmethods=GET,OPTIONS,POST"
- "traefik.http.middlewares.corsheaders2.headers.accesscontrolallowheaders=content-type"
- "traefik.http.middlewares.corsheaders2.headers.accesscontrolalloworiginlist=https://${HOST}"
- "traefik.http.middlewares.corsheaders2.headers.accesscontrolallowcredentials=true"
- "traefik.http.middlewares.corsheaders2.headers.accesscontrolmaxage=-1"
- "traefik.http.routers.spot.rule=Host(`${HOST}`) && PathPrefix(`/backend`)"
- "traefik.http.middlewares.stripprefix_spot.stripprefix.prefixes=/backend"
- "traefik.http.routers.spot.rule=Host(`${HOST}`) && PathPrefix(`/prod`)"
- "traefik.http.middlewares.stripprefix_spot.stripprefix.prefixes=/prod"
- "traefik.http.routers.spot.tls=true"
- "traefik.http.routers.spot.middlewares=corsheaders2,stripprefix_spot,auth"
- "traefik.http.routers.spot.middlewares=corsheaders2,stripprefix_spot,auth"

View File

@@ -11,4 +11,4 @@ for module in $PROJECT/modules/*.sh
do
log DEBUG "sourcing $module"
source $module
done
done

View File

@@ -66,6 +66,7 @@ services:
- HATEOAS_HOST=https://${HOST}
- CONNECTOR_TYPE=broker
- AUTHUP_URL=robot://system:${DNPM_AUTHUP_SECRET}@http://dnpm-authup:3000
- TZ=Europe/Berlin
volumes:
- /etc/bridgehead/dnpm/config:/dnpm_config
- /var/cache/bridgehead/dnpm/backend-data:/dnpm_data

View File

@@ -45,7 +45,6 @@ services:
BROKER_URL: ${BROKER_URL}
PROXY_ID: ${PROXY_ID}
APP_focus_KEY: ${FOCUS_BEAM_SECRET_SHORT}
APP_beamfilesend_KEY: ${BEAM_FILE_SEND_SECRET}
PRIVKEY_FILE: /run/secrets/proxy.pem
ALL_PROXY: http://forward_proxy:3128
TLS_CA_CERTIFICATES_DIR: /conf/trusted-ca-certs

View File

@@ -5,7 +5,6 @@ FOCUS_BEAM_SECRET_SHORT="$(cat /proc/sys/kernel/random/uuid | sed 's/[-]//g' | h
FOCUS_RETRY_COUNT=${FOCUS_RETRY_COUNT:-64}
SUPPORT_EMAIL=support-ccp@dkfz-heidelberg.de
PRIVATEKEYFILENAME=/etc/bridgehead/pki/${SITE_ID}.priv.pem
BEAM_FILE_SEND_SECRET="$(echo \"beam-file-send-salt\" | openssl pkeyutl -sign -inkey /etc/bridgehead/pki/${SITE_ID}.priv.pem | base64 | head -c 30)"
BROKER_URL_FOR_PREREQ=$BROKER_URL
@@ -25,5 +24,4 @@ do
done
transfairSetup
scoutSetup
beamFileSetup
scoutSetup

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@@ -0,0 +1,6 @@
#!/bin/bash
if [ -n "$ENABLE_OMICS" ];then
OVERRIDE+=" -f ./$PROJECT/modules/itcc-omics-ingest.yaml"
GENERATE_API_KEY="$(generate_simple_password 'omics')"
fi

View File

@@ -0,0 +1,14 @@
services:
omics-endpoint:
image: ghcr.io/samply/itcc-omics-ingest:main
environment:
- API_KEY=${GENERATE_API_KEY}
volumes:
- /var/cache/bridgehead/omics/data:/data/uploads
labels:
- "traefik.http.routers.omics.rule=Host(`${HOST}`) && PathPrefix(`/api/omics`)"
- "traefik.enable=true"
- "traefik.http.services.omics.loadbalancer.server.port=6080"
- "traefik.http.routers.omics.tls=true"
- "traefik.http.middlewares.omics-stripprefix.stripprefix.prefixes=/api"
- "traefik.http.routers.omics.middlewares=omics-stripprefix"

View File

@@ -1,32 +1,49 @@
version: "3.7"
services:
landing:
container_name: lens_federated-search
image: docker.verbis.dkfz.de/ccp/lens:${SITE_ID}
container_name: lens_itcc_explorer
image: ghcr.io/samply/itcc-explorer:fix-setup
environment:
HOST: "0.0.0.0"
BIND_ADDR: "0.0.0.0:3000"
PUBLIC_ENVIRONMENT: ${PUBLIC_ENVIRONMENT}
labels:
- "traefik.http.routers.lens.rule=Host(`${HOST}`)"
- "traefik.enable=true"
- "traefik.http.routers.landing.rule=PathPrefix(`/`)"
- "traefik.http.services.landing.loadbalancer.server.port=80"
- "traefik.http.services.landing.loadbalancer.server.port=3000"
- "traefik.http.routers.landing.tls=true"
spot:
image: docker.verbis.dkfz.de/ccp-private/central-spot
image: samply/rustyspot:latest
environment:
HTTP_PROXY: ${HTTP_PROXY_URL}
HTTPS_PROXY: ${HTTPS_PROXY_URL}
NO_PROXY: beam-proxy
BEAM_SECRET: "${FOCUS_BEAM_SECRET_SHORT}"
BEAM_URL: http://beam-proxy:8081
BEAM_PROXY_URL: http://beam-proxy:8081
BEAM_PROXY_ID: ${SITE_ID}
BEAM_BROKER_ID: ${BROKER_ID}
BEAM_APP_ID: "focus"
BEAM_APP_ID: "spot.${SITE_ID}.${BROKER_ID}"
CORS_ORIGIN: "https://${HOST}"
SITES: ${SITES}
TRANSFORM: LENS
PROJECT: "itcc"
BIND_ADDR: 0.0.0.0:8055
depends_on:
- "beam-proxy"
labels:
- "traefik.enable=true"
- "traefik.http.services.spot.loadbalancer.server.port=8080"
- "traefik.http.services.spot.loadbalancer.server.port=8055"
- "traefik.http.middlewares.corsheaders2.headers.accesscontrolallowmethods=GET,OPTIONS,POST"
- "traefik.http.middlewares.corsheaders2.headers.accesscontrolallowheaders=content-type"
- "traefik.http.middlewares.corsheaders2.headers.accesscontrolalloworiginlist=https://${HOST}"
- "traefik.http.middlewares.corsheaders2.headers.accesscontrolallowcredentials=true"
- "traefik.http.middlewares.corsheaders2.headers.accesscontrolmaxage=-1"
- "traefik.http.routers.spot.rule=Host(`${HOST}`) && PathPrefix(`/backend`)"
- "traefik.http.middlewares.stripprefix_spot.stripprefix.prefixes=/backend"
- "traefik.http.routers.spot.rule=Host(`${HOST}`) && PathPrefix(`/prod`)"
- "traefik.http.middlewares.stripprefix_spot.stripprefix.prefixes=/prod"
- "traefik.http.routers.spot.tls=true"
- "traefik.http.routers.spot.middlewares=corsheaders2,stripprefix_spot,auth"
beam-proxy:
environment:
APP_spot_KEY: ${FOCUS_BEAM_SECRET_SHORT}

View File

@@ -6,6 +6,8 @@ FOCUS_RETRY_COUNT=${FOCUS_RETRY_COUNT:-64}
SUPPORT_EMAIL=arturo.macias@dkfz-heidelberg.de
PRIVATEKEYFILENAME=/etc/bridgehead/pki/${SITE_ID}.priv.pem
BROKER_URL_FOR_PREREQ=$BROKER_URL
PUBLIC_ENVIRONMENT=prod
SITES=itcc-inform,itcc-ither,itcc-mappyacts,itcc-profyle,itcc-smpaeds,itcc-zero
for module in $PROJECT/modules/*.sh
do

View File

@@ -54,7 +54,7 @@ checkOwner(){
printUsage() {
echo "Usage: bridgehead start|stop|logs|docker-logs|is-running|update|check|install|uninstall|adduser|enroll PROJECTNAME"
echo "PROJECTNAME should be one of ccp|bbmri|cce|itcc|kr|dhki"
echo "PROJECTNAME should be one of ccp|bbmri|cce|itcc|kr|dhki|nngm"
}
checkRequirements() {
@@ -337,7 +337,7 @@ function sync_secrets() {
}
function secret_sync_gitlab_token() {
if [ "$PROJECT" == "minimal" ]; then
if [[ "$PROJECT" != "dktk" && "$PROJECT" != "bbmri" ]]; then
log "INFO" "Not running Secret Sync for project minimal"
return
fi

View File

@@ -55,6 +55,9 @@ case "$PROJECT" in
cce)
site_configuration_repository_middle="git.verbis.dkfz.de/cce-sites/"
;;
pscc)
site_configuration_repository_middle="git.verbis.dkfz.de/pscc-sites/"
;;
itcc)
site_configuration_repository_middle="git.verbis.dkfz.de/itcc-sites/"
;;
@@ -67,6 +70,9 @@ case "$PROJECT" in
dhki)
site_configuration_repository_middle="git.verbis.dkfz.de/dhki/"
;;
nngm)
site_configuration_repository_middle="git.verbis.dkfz.de/nngm/"
;;
minimal)
site_configuration_repository_middle="git.verbis.dkfz.de/minimal-bridgehead-configs/"
;;

View File

@@ -66,6 +66,7 @@ services:
- HATEOAS_HOST=https://${HOST}
- CONNECTOR_TYPE=broker
- AUTHUP_URL=robot://system:${DNPM_AUTHUP_SECRET}@http://dnpm-authup:3000
- TZ=Europe/Berlin
volumes:
- /etc/bridgehead/dnpm/config:/dnpm_config
- /var/cache/bridgehead/dnpm/backend-data:/dnpm_data

View File

@@ -1,35 +0,0 @@
# NOTE: Current implementation is restricted to a bridgehead only being able to either upload or download data
services:
beam-file-sender:
image: samply/beam-file:${BEAM_FILE_TAG}
container_name: bridgehead-beam-file-sender
environment:
- BEAM_ID=beamfilesend.${PROXY_ID}
- BEAM_SECRET=${BEAM_FILE_SEND_SECRET}
- BEAM_URL=http://beam-proxy:8081
- BIND_ADDR=0.0.0.0:8085
- API_KEY=${BEAM_FILE_API_KEY}
# Only uncomment if your are sure what to do
# ports:
# - 8085:8085
volumes:
- /var/cache/bridgehead/beam-file-out/:/data
profiles: ["beam-file-sender"]
beam-file-receiver:
image: samply/beam-file:${BEAM_FILE_TAG}
container_name: bridgehead-beam-file-receiver
environment:
- BEAM_ID=beamfile.${PROXY_ID}
- BEAM_SECRET=${BEAM_FILE_SECRET}
- BEAM_URL=http://beam-proxy:8081
- API_KEY=${BEAM_FILE_API_KEY}
command: ["receive", "save", "--outdir", "/data"]
volumes:
- /var/cache/bridgehead/beam-file/:/data
profiles: ["beam-file-receiver"]
beam-proxy:
environment:
APP_beamfile_KEY: ${BEAM_FILE_SECRET}
profiles: ["beam-file-receiver"]

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@@ -1,11 +0,0 @@
#!/bin/bash -e
function beamFileSetup() {
if [ -n "$ENABLE_BEAM_FILE_RECEIVER" ]; then
echo "Starting beam file in receiver mode"
OVERRIDE+=" -f ./modules/beam-file-compose.yml --profile beam-file-receiver"
BEAM_FILE_SECRET="$(cat /proc/sys/kernel/random/uuid | sed 's/[-]//g' | head -c 20)"
BEAM_FILE_API_KEY="$(cat /proc/sys/kernel/random/uuid | sed 's/[-]//g' | head -c 20)"
log INFO "Beam File in Receiver Mode available uses ApiKey ${BEAM_FILE_API_KEY}"
fi
}

65
nngm/docker-compose.yml Normal file
View File

@@ -0,0 +1,65 @@
version: "3.7"
services:
blaze:
image: docker.verbis.dkfz.de/cache/samply/blaze:${BLAZE_TAG}
container_name: bridgehead-nngm-blaze
environment:
BASE_URL: "http://bridgehead-nngm-blaze:8080"
JAVA_TOOL_OPTIONS: "-Xmx${BLAZE_MEMORY_CAP:-4096}m"
DB_RESOURCE_CACHE_SIZE: ${BLAZE_RESOURCE_CACHE_CAP:-2500000}
DB_BLOCK_CACHE_SIZE: ${BLAZE_MEMORY_CAP}
CQL_EXPR_CACHE_SIZE: ${BLAZE_CQL_CACHE_CAP:-32}
ENFORCE_REFERENTIAL_INTEGRITY: "false"
volumes:
- "blaze-data:/app/data"
labels:
- "traefik.enable=true"
- "traefik.http.routers.blaze_nngm.rule=PathPrefix(`/nngm-localdatamanagement`)"
- "traefik.http.middlewares.nngm_b_strip.stripprefix.prefixes=/nngm-localdatamanagement"
- "traefik.http.services.blaze_nngm.loadbalancer.server.port=8080"
- "traefik.http.routers.blaze_nngm.middlewares=nngm_b_strip,auth"
- "traefik.http.routers.blaze_nngm.tls=true"
focus:
image: docker.verbis.dkfz.de/cache/samply/focus:${FOCUS_TAG}
container_name: bridgehead-focus
environment:
- API_KEY=${FOCUS_BEAM_SECRET_SHORT}
- BEAM_APP_ID_LONG=focus.${PROXY_ID}
- PROXY_ID=${PROXY_ID}
- BLAZE_URL=http://bridgehead-nngm-blaze:8080/fhir/
- BEAM_PROXY_URL=http://beam-proxy:8081
- RETRY_COUNT=${FOCUS_RETRY_COUNT}
- EPSILON=0.28
- ENDPOINT_TYPE=${FOCUS_ENDPOINT_TYPE:-blaze}
- CQL_PROJECTS_ENABLED
depends_on:
- "beam-proxy"
- "blaze"
beam-proxy:
image: docker.verbis.dkfz.de/cache/samply/beam-proxy:${BEAM_TAG}
container_name: bridgehead-beam-proxy
environment:
BROKER_URL: ${BROKER_URL}
PROXY_ID: ${PROXY_ID}
APP_focus_KEY: ${FOCUS_BEAM_SECRET_SHORT}
PRIVKEY_FILE: /run/secrets/proxy.pem
ALL_PROXY: http://forward_proxy:3128
TLS_CA_CERTIFICATES_DIR: /conf/trusted-ca-certs
ROOTCERT_FILE: /conf/root.crt.pem
secrets:
- proxy.pem
depends_on:
- "forward_proxy"
volumes:
- /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro
- /srv/docker/bridgehead/nngm/root.crt.pem:/conf/root.crt.pem:ro
volumes:
blaze-data:
secrets:
proxy.pem:
file: /etc/bridgehead/pki/${SITE_ID}.priv.pem

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@@ -0,0 +1,72 @@
version: "3.7"
services:
exporter:
image: docker.verbis.dkfz.de/ccp/dktk-exporter:latest
container_name: bridgehead-nngm-exporter
environment:
JAVA_OPTS: "-Xms1G -Xmx8G -XX:+UseG1GC"
LOG_LEVEL: "INFO"
EXPORTER_API_KEY: "${EXPORTER_API_KEY}" # Set in exporter-setup.sh
CROSS_ORIGINS: "https://${HOST}"
EXPORTER_DB_USER: "exporter"
EXPORTER_DB_PASSWORD: "${EXPORTER_DB_PASSWORD}" # Set in exporter-setup.sh
EXPORTER_DB_URL: "jdbc:postgresql://exporter-db:5432/exporter"
HTTP_RELATIVE_PATH: "/nngm-exporter"
SITE: "${SITE_ID}"
HTTP_SERVLET_REQUEST_SCHEME: "https"
OPAL_PASSWORD: "${EXPORTER_OPAL_PASSWORD}"
labels:
- "traefik.enable=true"
- "traefik.http.routers.exporter_nngm.rule=PathPrefix(`/nngm-exporter`)"
- "traefik.http.services.exporter_nngm.loadbalancer.server.port=8092"
- "traefik.http.routers.exporter_nngm.tls=true"
- "traefik.http.middlewares.exporter_nngm_strip.stripprefix.prefixes=/nngm-exporter"
- "traefik.http.routers.exporter_nngm.middlewares=exporter_nngm_strip"
volumes:
- "/var/cache/bridgehead/nngm/exporter-files:/app/exporter-files/output"
exporter-db:
image: docker.verbis.dkfz.de/cache/postgres:${POSTGRES_TAG}
container_name: bridgehead-nngm-exporter-db
environment:
POSTGRES_USER: "exporter"
POSTGRES_PASSWORD: "${EXPORTER_DB_PASSWORD}" # Set in exporter-setup.sh
POSTGRES_DB: "exporter"
volumes:
# Consider removing this volume once we find a solution to save Lens-queries to be executed in the explorer.
- "/var/cache/bridgehead/nngm/exporter-db:/var/lib/postgresql/data"
reporter:
image: docker.verbis.dkfz.de/ccp/dktk-reporter:latest
container_name: bridgehead-nngm-reporter
environment:
JAVA_OPTS: "-Xms1G -Xmx8G -XX:+UseG1GC"
LOG_LEVEL: "INFO"
CROSS_ORIGINS: "https://${HOST}"
HTTP_RELATIVE_PATH: "/nngm-reporter"
SITE: "${SITE_ID}"
EXPORTER_API_KEY: "${EXPORTER_API_KEY}" # Set in exporter-setup.sh
EXPORTER_URL: "http://exporter:8092"
LOG_FHIR_VALIDATION: "false"
HTTP_SERVLET_REQUEST_SCHEME: "https"
# In this initial development state of the bridgehead, we are trying to have so many volumes as possible.
# However, in the first executions in the CCP sites, this volume seems to be very important. A report is
# a process that can take several hours, because it depends on the exporter.
# There is a risk that the bridgehead restarts, losing the already created export.
volumes:
- "/var/cache/bridgehead/nngm/reporter-files:/app/reports"
labels:
- "traefik.enable=true"
- "traefik.http.routers.reporter_nngm.rule=PathPrefix(`/nngm-reporter`)"
- "traefik.http.services.reporter_nngm.loadbalancer.server.port=8095"
- "traefik.http.routers.reporter_nngm.tls=true"
- "traefik.http.middlewares.reporter_nngm_strip.stripprefix.prefixes=/nngm-reporter"
- "traefik.http.routers.reporter_nngm.middlewares=reporter_nngm_strip"
focus:
environment:
EXPORTER_URL: "http://exporter:8092"
EXPORTER_API_KEY: "${EXPORTER_API_KEY}"

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@@ -0,0 +1,8 @@
#!/bin/bash -e
if [ "$ENABLE_EXPORTER" == true ]; then
log INFO "Exporter setup detected -- will start Exporter service."
OVERRIDE+=" -f ./$PROJECT/modules/exporter-compose.yml"
EXPORTER_DB_PASSWORD="$(echo \"This is a salt string to generate one consistent password for the exporter. It is not required to be secret.\" | sha1sum | openssl pkeyutl -sign -inkey /etc/bridgehead/pki/${SITE_ID}.priv.pem | base64 | head -c 30)"
EXPORTER_API_KEY="$(echo \"This is a salt string to generate one consistent API KEY for the exporter. It is not required to be secret.\" | sha1sum | openssl pkeyutl -sign -inkey /etc/bridgehead/pki/${SITE_ID}.priv.pem | base64 | head -c 64)"
fi

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@@ -0,0 +1,73 @@
version: "3.7"
services:
teiler-orchestrator:
image: docker.verbis.dkfz.de/cache/samply/teiler-orchestrator:latest
container_name: bridgehead-teiler-orchestrator
labels:
- "traefik.enable=true"
- "traefik.http.routers.teiler_orchestrator_nngm.rule=PathPrefix(`/nngm-teiler`)"
- "traefik.http.services.teiler_orchestrator_nngm.loadbalancer.server.port=9000"
- "traefik.http.routers.teiler_orchestrator_nngm.tls=true"
- "traefik.http.middlewares.teiler_orchestrator_nngm_strip.stripprefix.prefixes=/nngm-teiler"
- "traefik.http.routers.teiler_orchestrator_nngm.middlewares=teiler_orchestrator_nngm_strip"
environment:
TEILER_BACKEND_URL: "/nngm-teiler-backend"
TEILER_DASHBOARD_URL: "/nngm-teiler-dashboard"
DEFAULT_LANGUAGE: "${TEILER_DEFAULT_LANGUAGE_LOWER_CASE}"
HTTP_RELATIVE_PATH: "/nngm-teiler"
teiler-dashboard:
image: docker.verbis.dkfz.de/cache/samply/teiler-dashboard:${TEILER_DASHBOARD_TAG}
container_name: bridgehead-teiler-dashboard
labels:
- "traefik.enable=true"
- "traefik.http.routers.teiler_dashboard_nngm.rule=PathPrefix(`/nngm-teiler-dashboard`)"
- "traefik.http.services.teiler_dashboard_nngm.loadbalancer.server.port=80"
- "traefik.http.routers.teiler_dashboard_nngm.tls=true"
- "traefik.http.middlewares.teiler_dashboard_nngm_strip.stripprefix.prefixes=/nngm-teiler-dashboard"
- "traefik.http.routers.teiler_dashboard_nngm.middlewares=teiler_dashboard_nngm_strip"
environment:
DEFAULT_LANGUAGE: "${TEILER_DEFAULT_LANGUAGE}"
TEILER_BACKEND_URL: "/nngm-teiler-backend"
TEILER_DASHBOARD_URL: "/nngm-teiler-dashboard"
OIDC_URL: "${OIDC_URL}"
OIDC_CLIENT_ID: "${OIDC_PUBLIC_CLIENT_ID}"
OIDC_TOKEN_GROUP: "${OIDC_GROUP_CLAIM}"
TEILER_ADMIN_NAME: "${OPERATOR_FIRST_NAME} ${OPERATOR_LAST_NAME}"
TEILER_ADMIN_EMAIL: "${OPERATOR_EMAIL}"
TEILER_ADMIN_PHONE: "${OPERATOR_PHONE}"
TEILER_PROJECT: "${PROJECT}"
EXPORTER_API_KEY: "${EXPORTER_API_KEY}"
TEILER_ORCHESTRATOR_URL: "/nngm-teiler"
TEILER_ORCHESTRATOR_HTTP_RELATIVE_PATH: "/nngm-teiler"
TEILER_USER: "${OIDC_USER_GROUP}"
TEILER_ADMIN: "${OIDC_ADMIN_GROUP}"
REPORTER_DEFAULT_TEMPLATE_ID: "ccp-qb"
EXPORTER_DEFAULT_TEMPLATE_ID: "ccp"
# TODO: Replace dktk-teiler-backend with nngm-teiler-backend
teiler-backend:
image: docker.verbis.dkfz.de/ccp/dktk-teiler-backend:latest
container_name: bridgehead-teiler-backend
labels:
- "traefik.enable=true"
- "traefik.http.routers.teiler_backend_nngm.rule=PathPrefix(`/nngm-teiler-backend`)"
- "traefik.http.services.teiler_backend_nngm.loadbalancer.server.port=8085"
- "traefik.http.routers.teiler_backend_nngm.tls=true"
- "traefik.http.middlewares.teiler_backend_nngm_strip.stripprefix.prefixes=/nngm-teiler-backend"
- "traefik.http.routers.teiler_backend_nngm.middlewares=teiler_backend_nngm_strip"
environment:
LOG_LEVEL: "INFO"
APPLICATION_PORT: "8085"
DEFAULT_LANGUAGE: "${TEILER_DEFAULT_LANGUAGE}"
TEILER_ORCHESTRATOR_HTTP_RELATIVE_PATH: "/nngm-teiler"
TEILER_ORCHESTRATOR_URL: "/nngm-teiler"
TEILER_DASHBOARD_DE_URL: "/nngm-teiler-dashboard/de"
TEILER_DASHBOARD_EN_URL: "/nngm-teiler-dashboard/en"
HTTP_PROXY: "http://forward_proxy:3128"
ENABLE_MTBA: "${ENABLE_MTBA}"
ENABLE_DATASHIELD: "${ENABLE_DATASHIELD}"
IDMANAGER_UPLOAD_APIKEY: "${IDMANAGER_UPLOAD_APIKEY}" # Only used to check if the ID Manager is active

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@@ -0,0 +1,8 @@
#!/bin/bash -e
if [ "$ENABLE_TEILER" == true ];then
log INFO "Teiler setup detected -- will start Teiler services."
OVERRIDE+=" -f ./$PROJECT/modules/teiler-compose.yml"
TEILER_DEFAULT_LANGUAGE=DE
TEILER_DEFAULT_LANGUAGE_LOWER_CASE=${TEILER_DEFAULT_LANGUAGE,,}
fi

20
nngm/root.crt.pem Normal file
View File

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

32
nngm/vars Normal file
View File

@@ -0,0 +1,32 @@
BROKER_ID=broker.nngm.dkfz.de
BROKER_URL=https://${BROKER_ID}
PROXY_ID=${SITE_ID}.${BROKER_ID}
FOCUS_BEAM_SECRET_SHORT="$(cat /proc/sys/kernel/random/uuid | sed 's/[-]//g' | head -c 20)"
FOCUS_RETRY_COUNT=${FOCUS_RETRY_COUNT:-64}
# TODO: Add real nNGM-Support email
SUPPORT_EMAIL=support-nngm@dkfz-heidelberg.de
PRIVATEKEYFILENAME=/etc/bridgehead/pki/${SITE_ID}.priv.pem
BROKER_URL_FOR_PREREQ=$BROKER_URL
# TODO: Replace with nNGM OIDC Server
OIDC_USER_GROUP="NNGM_$(capitalize_first_letter ${SITE_ID})"
OIDC_ADMIN_GROUP="NNGM_$(capitalize_first_letter ${SITE_ID})_Verwalter"
OIDC_PSP_GROUP="NNGM_$(capitalize_first_letter ${SITE_ID})_PSP"
OIDC_PRIVATE_CLIENT_ID=${SITE_ID}-private
OIDC_PUBLIC_CLIENT_ID=${SITE_ID}-public
OIDC_URL="https://sso.verbis.dkfz.de/application/o/${OIDC_PUBLIC_CLIENT_ID}/"
OIDC_PRIVATE_URL="https://sso.verbis.dkfz.de/application/o/${OIDC_PRIVATE_CLIENT_ID}/"
OIDC_GROUP_CLAIM="groups"
for module in $PROJECT/modules/*.sh
do
log DEBUG "sourcing $module"
source $module
done
for module in modules/*.sh
do
log DEBUG "sourcing $module"
source $module
done

67
pscc/docker-compose.yml Normal file
View File

@@ -0,0 +1,67 @@
version: "3.7"
services:
blaze:
image: docker.verbis.dkfz.de/cache/samply/blaze:${BLAZE_TAG}
container_name: bridgehead-pscc-blaze
environment:
BASE_URL: "http://bridgehead-pscc-blaze:8080"
JAVA_TOOL_OPTIONS: "-Xmx${BLAZE_MEMORY_CAP:-4096}m"
DB_RESOURCE_CACHE_SIZE: ${BLAZE_RESOURCE_CACHE_CAP:-2500000}
DB_BLOCK_CACHE_SIZE: ${BLAZE_MEMORY_CAP}
CQL_EXPR_CACHE_SIZE: ${BLAZE_CQL_CACHE_CAP:-32}
ENFORCE_REFERENTIAL_INTEGRITY: "false"
volumes:
- "blaze-data:/app/data"
labels:
- "traefik.enable=true"
- "traefik.http.routers.blaze_pscc.rule=PathPrefix(`/pscc-localdatamanagement`)"
- "traefik.http.middlewares.pscc_b_strip.stripprefix.prefixes=/pscc-localdatamanagement"
- "traefik.http.services.blaze_pscc.loadbalancer.server.port=8080"
- "traefik.http.routers.blaze_pscc.middlewares=pscc_b_strip,auth"
- "traefik.http.routers.blaze_pscc.tls=true"
focus:
image: docker.verbis.dkfz.de/cache/samply/focus:${FOCUS_TAG}
container_name: bridgehead-focus
environment:
API_KEY: ${FOCUS_BEAM_SECRET_SHORT}
BEAM_APP_ID_LONG: focus.${PROXY_ID}
PROXY_ID: ${PROXY_ID}
BLAZE_URL: "http://bridgehead-pscc-blaze:8080/fhir/"
BEAM_PROXY_URL: http://beam-proxy:8081
RETRY_COUNT: ${FOCUS_RETRY_COUNT}
EPSILON: 0.28
ENDPOINT_TYPE: ${FOCUS_ENDPOINT_TYPE:-blaze}
depends_on:
- "beam-proxy"
- "blaze"
beam-proxy:
image: docker.verbis.dkfz.de/cache/samply/beam-proxy:${BEAM_TAG}
container_name: bridgehead-beam-proxy
environment:
BROKER_URL: ${BROKER_URL}
PROXY_ID: ${PROXY_ID}
APP_focus_KEY: ${FOCUS_BEAM_SECRET_SHORT}
PRIVKEY_FILE: /run/secrets/proxy.pem
ALL_PROXY: http://forward_proxy:3128
TLS_CA_CERTIFICATES_DIR: /conf/trusted-ca-certs
ROOTCERT_FILE: /conf/root.crt.pem
secrets:
- proxy.pem
depends_on:
- "forward_proxy"
volumes:
- /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro
- /srv/docker/bridgehead/pscc/root.crt.pem:/conf/root.crt.pem:ro
landing:
profiles: [deactivated]
volumes:
blaze-data:
secrets:
proxy.pem:
file: /etc/bridgehead/pki/${SITE_ID}.priv.pem

View File

@@ -0,0 +1,40 @@
version: "3.7"
services:
lens:
container_name: lens-federated-search
image: docker.verbis.dkfz.de/ccp/lens:${SITE_ID}
labels:
- "traefik.http.services.lens.loadbalancer.server.port=3000"
- "traefik.enable=true"
- "traefik.http.routers.lens.rule=Host(`${HOST}`)"
- "traefik.http.routers.lens.tls=true"
spot:
image: samply/rustyspot:latest
platform: linux/amd64
environment:
HTTP_PROXY: ${HTTP_PROXY_URL}
HTTPS_PROXY: ${HTTPS_PROXY_URL}
NO_PROXY: beam-proxy
BEAM_SECRET: "${FOCUS_BEAM_SECRET_SHORT}"
BEAM_PROXY_URL: http://beam-proxy:8081
BEAM_APP_ID: "spot.${SITE_ID}.${BROKER_ID}"
CORS_ORIGIN: "https://${HOST}"
SITES: ${SITES}
TRANSFORM: LENS
PROJECT: pscc
BIND_ADDR: 0.0.0.0:8055
depends_on:
- "beam-proxy"
labels:
- "traefik.enable=true"
- "traefik.http.services.spot.loadbalancer.server.port=8055"
- "traefik.http.middlewares.corsheaders2.headers.accesscontrolallowmethods=GET,OPTIONS,POST"
- "traefik.http.middlewares.corsheaders2.headers.accesscontrolallowheaders=content-type"
- "traefik.http.middlewares.corsheaders2.headers.accesscontrolalloworiginlist=https://${HOST}"
- "traefik.http.middlewares.corsheaders2.headers.accesscontrolallowcredentials=true"
- "traefik.http.middlewares.corsheaders2.headers.accesscontrolmaxage=-1"
- "traefik.http.routers.spot.rule=Host(`${HOST}`) && PathPrefix(`/prod`)"
- "traefik.http.middlewares.stripprefix_spot.stripprefix.prefixes=/prod"
- "traefik.http.routers.spot.tls=true"
- "traefik.http.routers.spot.middlewares=corsheaders2,stripprefix_spot,auth"

View File

@@ -0,0 +1,5 @@
#!/bin/bash
if [ -n "$ENABLE_LENS" ];then
OVERRIDE+=" -f ./$PROJECT/modules/lens-compose.yml"
fi

20
pscc/root.crt.pem Normal file
View File

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

14
pscc/vars Normal file
View File

@@ -0,0 +1,14 @@
BROKER_ID=test-no-real-data.broker.samply.de
BROKER_URL=https://${BROKER_ID}
PROXY_ID=${SITE_ID}.${BROKER_ID}
FOCUS_BEAM_SECRET_SHORT="$(cat /proc/sys/kernel/random/uuid | sed 's/[-]//g' | head -c 20)"
FOCUS_RETRY_COUNT=${FOCUS_RETRY_COUNT:-64}
SUPPORT_EMAIL=denis.koether@dkfz-heidelberg.de
PRIVATEKEYFILENAME=/etc/bridgehead/pki/${SITE_ID}.priv.pem
BROKER_URL_FOR_PREREQ=$BROKER_URL
for module in $PROJECT/modules/*.sh
do
log DEBUG "sourcing $module"
source $module
done

View File

@@ -3,5 +3,4 @@ BEAM_TAG=develop
BLAZE_TAG=main
POSTGRES_TAG=15.13-alpine
TEILER_DASHBOARD_TAG=develop
MTBA_TAG=develop
BEAM_FILE_TAG=task-based-files
MTBA_TAG=develop