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23 Commits

Author SHA1 Message Date
d43f6822bc fix landingpage 2024-09-12 11:42:45 +00:00
Jan
02ee84df2c Merge pull request #183 from samply/fix/minimal-checks
Dont test clock skew and priv key for minimal bridgeheads
2024-04-26 09:04:40 +02:00
36c5c1a080 Changed dnpm-configuration to allow different broker 2024-03-06 13:21:11 +00:00
b5c35211f6 Dont test clock skew and priv key for minimal bridgeheads 2024-03-05 14:58:06 +00:00
48e198fa0c Merge pull request #159 from samply/feat/dnpm-test-data-generation
Create env to control dnpm synthetic data generation
2024-02-29 08:18:13 +01:00
ad4430e480 Create env to control dnpm synthetic data generation 2024-02-28 10:11:03 +00:00
443dcc6ec2 Merge pull request #157 from samply/fix/set-focus-version
fix: set focus version to 0.4.0
2024-02-28 10:56:00 +01:00
b2c933f5e5 fix: set focus version to 0.4.0 2024-02-28 10:52:57 +01:00
c58096aa27 Merge pull request #155 from samply/fix/dnpm-no-proxy
Add DNPM_NO_PROXY configuration option
2024-02-23 11:37:47 +01:00
5470fd726a Merge pull request #156 from samply/fix/dnpm-beam-connect-trusted-certs
mount and process trusted certs in dnpm-beam-connect
2024-02-22 19:25:02 +01:00
3f6e3a2bb4 mount and process trusted certs in dnpm-beam-connect 2024-02-22 15:41:11 +00:00
9937002d06 Add DNPM_NO_PROXY configuration option 2024-02-21 15:04:00 +00:00
a1d0e93106 Merge pull request #153 from samply/dnpm-not-in-bbmri
Remove DNPM code from BBMRI
2024-02-20 16:46:47 +01:00
f367a406bb Remove DNPM code from BBMRI 2024-02-20 10:47:42 +01:00
8854670f4d Merge pull request #152 from samply/feature/dnpm-echo
Add dnpm echo to dnpm-compose
2024-02-20 10:36:26 +01:00
aac31945a3 Add dnpm echo to dnpm-compose 2024-02-19 08:50:15 +00:00
60b2bddf15 Merge pull request #146 from samply/fix/updates
Fix image updates for image names with vars
2024-02-14 16:37:28 +01:00
d8da5da7eb Merge pull request #150 from samply/feature/bridgehead-logs
Add `bridgehead logs` command
2024-02-14 16:25:41 +01:00
16fc40f8ae feat: Add bridgehead logs command 2024-02-14 14:43:17 +00:00
001b84a774 Revert "Merge pull request #147 from samply/fix/set-focus-version-to-main"
This reverts commit 6550c0cdab, reversing
changes made to 40d991d94e.
2024-02-12 08:55:29 +00:00
ed0bd483dd Use backwards compatible compose config version 2024-02-12 08:54:15 +00:00
5516ad7641 Add project 2024-02-12 08:54:15 +00:00
d44ff4055f fix(updates): Use docker compose config to list images 2024-02-12 08:54:15 +00:00
47 changed files with 108 additions and 1081 deletions

2
.gitignore vendored
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@ -1,7 +1,7 @@
##Ignore site configuration
.gitmodules
site-config/*
.idea
## Ignore site configuration
*/docker-compose.override.yml

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@ -1,5 +1,3 @@
version: "3.7"
services:
directory_sync_service:
image: "docker.verbis.dkfz.de/cache/samply/directory_sync_service"

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@ -1,53 +0,0 @@
version: "3.7"
services:
dnpm-beam-proxy:
image: docker.verbis.dkfz.de/cache/samply/beam-proxy:develop
container_name: bridgehead-dnpm-beam-proxy
environment:
BROKER_URL: ${DNPM_BROKER_URL}
PROXY_ID: ${DNPM_PROXY_ID}
APP_dnpm-connect_KEY: ${DNPM_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/ccp/root.crt.pem:/conf/root.crt.pem:ro
dnpm-beam-connect:
depends_on: [ dnpm-beam-proxy ]
image: docker.verbis.dkfz.de/cache/samply/beam-connect:develop
container_name: bridgehead-dnpm-beam-connect
environment:
PROXY_URL: http://dnpm-beam-proxy:8081
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"
HTTP_PROXY: http://forward_proxy:3128
HTTPS_PROXY: http://forward_proxy:3128
NO_PROXY: dnpm-beam-proxy,dnpm-backend, host.docker.internal
RUST_LOG: ${RUST_LOG:-info}
NO_AUTH: "true"
extra_host:
- "host.docker.internal:host-gateway"
volumes:
- /etc/bridgehead/dnpm/local_targets.json:/conf/connect_targets.json:ro
- /etc/bridgehead/dnpm/central_targets.json:/conf/central_targets.json:ro
labels:
- "traefik.enable=true"
- "traefik.http.routers.dnpm-connect.rule=PathPrefix(`/dnpm-connect`)"
- "traefik.http.middlewares.dnpm-connect-strip.stripprefix.prefixes=/dnpm-connect"
- "traefik.http.routers.dnpm-connect.middlewares=dnpm-connect-strip"
- "traefik.http.services.dnpm-connect.loadbalancer.server.port=8062"
- "traefik.http.routers.dnpm-connect.tls=true"
secrets:
proxy.pem:
file: /etc/bridgehead/pki/${SITE_ID}.priv.pem

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@ -1,33 +0,0 @@
version: "3.7"
services:
dnpm-backend:
image: ghcr.io/kohlbacherlab/bwhc-backend:1.0-snapshot-broker-connector
container_name: bridgehead-dnpm-backend
environment:
- ZPM_SITE=${ZPM_SITE}
volumes:
- /etc/bridgehead/dnpm:/bwhc_config:ro
- ${DNPM_DATA_DIR}:/bwhc_data
labels:
- "traefik.enable=true"
- "traefik.http.routers.bwhc-backend.rule=PathPrefix(`/bwhc`)"
- "traefik.http.services.bwhc-backend.loadbalancer.server.port=9000"
- "traefik.http.routers.bwhc-backend.tls=true"
dnpm-frontend:
image: ghcr.io/kohlbacherlab/bwhc-frontend:2209
container_name: bridgehead-dnpm-frontend
links:
- dnpm-backend
environment:
- NUXT_HOST=0.0.0.0
- NUXT_PORT=8080
- BACKEND_PROTOCOL=https
- BACKEND_HOSTNAME=$HOST
- BACKEND_PORT=443
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"

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@ -1,27 +0,0 @@
#!/bin/bash
if [ -n "${ENABLE_DNPM_NODE}" ]; then
log INFO "DNPM setup detected (BwHC Node) -- will start BwHC node."
OVERRIDE+=" -f ./$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
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
fi

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@ -1,12 +0,0 @@
#!/bin/bash
if [ -n "${ENABLE_DNPM}" ]; then
log INFO "DNPM setup detected (Beam.Connect) -- will start Beam and Beam.Connect for DNPM."
OVERRIDE+=" -f ./$PROJECT/modules/dnpm-compose.yml"
# Set variables required for Beam-Connect
DNPM_BEAM_SECRET_SHORT="$(cat /proc/sys/kernel/random/uuid | sed 's/[-]//g' | head -c 20)"
DNPM_BROKER_ID="broker.ccp-it.dktk.dkfz.de"
DNPM_BROKER_URL="https://${DNPM_BROKER_ID}"
DNPM_PROXY_ID="${SITE_ID}.${DNPM_BROKER_ID}"
fi

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@ -41,7 +41,6 @@ case "$PROJECT" in
;;
esac
# TODO: Please add proper documentation for variable priorities (1. secrets, 2. vars, 3. PROJECT.local.conf, 4. PROJECT.conf, 5. ???
loadVars() {
# Load variables from /etc/bridgehead and /srv/docker/bridgehead
set -a
@ -51,7 +50,6 @@ loadVars() {
source /etc/bridgehead/$PROJECT.local.conf || fail_and_report 1 "Found /etc/bridgehead/$PROJECT.local.conf but failed to import"
fi
fetchVarsFromVaultByFile /etc/bridgehead/$PROJECT.conf || fail_and_report 1 "Unable to fetchVarsFromVaultByFile"
setHostname
[ -e ./$PROJECT/vars ] && source ./$PROJECT/vars
set +a
@ -66,6 +64,7 @@ loadVars() {
OVERRIDE+=" -f ./$PROJECT/docker-compose.override.yml"
fi
detectCompose
setHostname
setupProxy
# Set some project-independent default values
@ -90,7 +89,6 @@ case "$ACTION" in
loadVars
hc_send log "Bridgehead $PROJECT startup: Checking requirements ..."
checkRequirements
sync_secrets
hc_send log "Bridgehead $PROJECT startup: Requirements checked out. Now starting bridgehead ..."
exec $COMPOSE -p $PROJECT -f ./minimal/docker-compose.yml -f ./$PROJECT/docker-compose.yml $OVERRIDE up --abort-on-container-exit
;;
@ -104,6 +102,11 @@ case "$ACTION" in
bk_is_running
exit $?
;;
logs)
loadVars
shift 2
exec $COMPOSE -p $PROJECT -f ./minimal/docker-compose.yml -f ./$PROJECT/docker-compose.yml $OVERRIDE logs -f $@
;;
update)
loadVars
exec ./lib/update-bridgehead.sh $PROJECT

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@ -19,7 +19,7 @@ services:
- "traefik.http.routers.blaze_ccp.tls=true"
focus:
image: docker.verbis.dkfz.de/cache/samply/focus:main
image: docker.verbis.dkfz.de/cache/samply/focus:0.4.0
container_name: bridgehead-focus
environment:
API_KEY: ${FOCUS_BEAM_SECRET_SHORT}
@ -52,12 +52,6 @@ services:
- /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro
- /srv/docker/bridgehead/ccp/root.crt.pem:/conf/root.crt.pem:ro
traefik:
labels:
- "traefik.http.middlewares.oidcAuth.forwardAuth.address=http://oauth2_proxy:4180/"
- "traefik.http.middlewares.oidcAuth.forwardAuth.trustForwardHeader=true"
- "traefik.http.middlewares.oidcAuth.forwardAuth.authResponseHeaders=X-Auth-Request-Access-Token,Authorization"
volumes:
blaze-data:

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@ -1,53 +0,0 @@
version: '3.7'
services:
cbioportal:
# image: docker.verbis.dkfz.de/ccp/dktk-cbioportal:latest
image: dktk-cbioportal
container_name: bridgehead-cbioportal
environment:
DB_PASSWORD: ${CBIOPORTAL_DB_PASSWORD}
HTTP_RELATIVE_PATH: "/cbioportal"
UPLOAD_HTTP_RELATIVE_PATH: "/cbioportal-upload"
depends_on:
- cbioportal-database
- cbioportal-session
labels:
- "traefik.enable=true"
- "traefik.http.routers.cbioportal.rule=PathPrefix(`/cbioportal`)"
- "traefik.http.routers.cbioportal.service=cbioportal"
- "traefik.http.services.cbioportal.loadbalancer.server.port=8080"
- "traefik.http.routers.cbioportal.tls=true"
- "traefik.http.routers.cbioportal-upload.rule=PathPrefix(`/cbioportal-upload`)"
- "traefik.http.routers.cbioportal-upload.service=cbioportal-upload"
- "traefik.http.routers.cbioportal-upload.tls=true"
- "traefik.http.services.cbioportal-upload.loadbalancer.server.port=8001"
cbioportal-database:
image: docker.verbis.dkfz.de/ccp/dktk-cbioportal-database:latest
container_name: bridgehead-cbioportal-database
environment:
MYSQL_DATABASE: cbioportal
MYSQL_USER: cbio_user
MYSQL_PASSWORD: ${CBIOPORTAL_DB_PASSWORD}
MYSQL_ROOT_PASSWORD: ${CBIOPORTAL_DB_ROOT_PASSWORD}
volumes:
- /var/cache/bridgehead/ccp/cbioportal_db_data:/var/lib/mysql
cbioportal-session:
image: cbioportal/session-service:0.6.1
container_name: bridgehead-cbioportal-session
environment:
SERVER_PORT: 5000
JAVA_OPTS: -Dspring.data.mongodb.uri=mongodb://cbioportal-session-database:27017/session-service
depends_on:
- cbioportal-session-database
cbioportal-session-database:
image: mongo:4.2
container_name: bridgehead-cbioportal-session-database
environment:
MONGO_INITDB_DATABASE: session_service
volumes:
- /var/cache/bridgehead/ccp/cbioportal_session_db_data:/data/db

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

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@ -1,10 +0,0 @@
# CBioPortal Data uploader
## Usage
We have integrated an API that allows you to upload data directly to cbioportal without the need to have cbioportal installed in your system.
## Tech stack
We used Flask to add this feature

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@ -1,161 +0,0 @@
version: "3.7"
services:
rstudio:
container_name: bridgehead-rstudio
image: docker.verbis.dkfz.de/ccp/dktk-rstudio:latest
environment:
#DEFAULT_USER: "rstudio" # This line is kept for informational purposes
PASSWORD: "${RSTUDIO_ADMIN_PASSWORD}" # It is required, even if the authentication is disabled
DISABLE_AUTH: "true" # https://rocker-project.org/images/versioned/rstudio.html#how-to-use
HTTP_RELATIVE_PATH: "/rstudio"
ALL_PROXY: "http://forward_proxy:3128" # https://rocker-project.org/use/networking.html
labels:
- "traefik.enable=true"
- "traefik.http.routers.rstudio_ccp.rule=PathPrefix(`/rstudio`)"
- "traefik.http.services.rstudio_ccp.loadbalancer.server.port=8787"
- "traefik.http.middlewares.rstudio_ccp_strip.stripprefix.prefixes=/rstudio"
- "traefik.http.routers.rstudio_ccp.tls=true"
- "traefik.http.routers.rstudio_ccp.middlewares=oidcAuth,rstudio_ccp_strip"
networks:
- rstudio
opal:
container_name: bridgehead-opal
image: docker.verbis.dkfz.de/ccp/dktk-opal:latest
labels:
- "traefik.enable=true"
- "traefik.http.routers.opal_ccp.rule=PathPrefix(`/opal`)"
- "traefik.http.services.opal_ccp.loadbalancer.server.port=8080"
- "traefik.http.routers.opal_ccp.tls=true"
links:
- opal-rserver
- opal-db
environment:
JAVA_OPTS: "-Xms1G -Xmx8G -XX:+UseG1GC -Dhttps.proxyHost=forward_proxy -Dhttps.proxyPort=3128"
# OPAL_ADMINISTRATOR_USER: "administrator" # This line is kept for informational purposes
OPAL_ADMINISTRATOR_PASSWORD: "${OPAL_ADMIN_PASSWORD}"
POSTGRESDATA_HOST: "opal-db"
POSTGRESDATA_DATABASE: "opal"
POSTGRESDATA_USER: "opal"
POSTGRESDATA_PASSWORD: "${OPAL_DB_PASSWORD}"
ROCK_HOSTS: "opal-rserver:8085"
APP_URL: "https://${HOST}/opal"
APP_CONTEXT_PATH: "/opal"
OPAL_PRIVATE_KEY: "/run/secrets/opal-key.pem"
OPAL_CERTIFICATE: "/run/secrets/opal-cert.pem"
KEYCLOAK_URL: "${KEYCLOAK_URL}"
KEYCLOAK_REALM: "${KEYCLOAK_REALM}"
KEYCLOAK_CLIENT_ID: "${KEYCLOAK_PRIVATE_CLIENT_ID}"
KEYCLOAK_CLIENT_SECRET: "${OIDC_CLIENT_SECRET}"
KEYCLOAK_ADMIN_GROUP: "${KEYCLOAK_ADMIN_GROUP}"
TOKEN_MANAGER_PASSWORD: "${TOKEN_MANAGER_OPAL_PASSWORD}"
EXPORTER_PASSWORD: "${EXPORTER_OPAL_PASSWORD}"
BEAM_APP_ID: token-manager.${PROXY_ID}
BEAM_SECRET: ${TOKEN_MANAGER_SECRET}
BEAM_DATASHIELD_PROXY: request-manager
volumes:
- "/var/cache/bridgehead/ccp/opal-metadata-db:/srv" # Opal metadata
secrets:
- opal-cert.pem
- opal-key.pem
opal-db:
container_name: bridgehead-opal-db
image: docker.verbis.dkfz.de/cache/postgres:15.4-alpine
environment:
POSTGRES_PASSWORD: "${OPAL_DB_PASSWORD}" # Set in datashield-setup.sh
POSTGRES_USER: "opal"
POSTGRES_DB: "opal"
volumes:
- "/var/cache/bridgehead/ccp/opal-db:/var/lib/postgresql/data" # Opal project data (imported from exporter)
opal-rserver:
container_name: bridgehead-opal-rserver
image: docker.verbis.dkfz.de/ccp/dktk-rserver # datashield/rock-base + dsCCPhos
tmpfs:
- /srv
beam-connect:
image: docker.verbis.dkfz.de/cache/samply/beam-connect:develop
container_name: bridgehead-datashield-connect
environment:
PROXY_URL: "http://beam-proxy:8081"
TLS_CA_CERTIFICATES_DIR: /run/secrets
APP_ID: datashield-connect.${SITE_ID}.${BROKER_ID}
PROXY_APIKEY: ${DATASHIELD_CONNECT_SECRET}
DISCOVERY_URL: "./map/central.json"
LOCAL_TARGETS_FILE: "./map/local.json"
NO_AUTH: "true"
secrets:
- opal-cert.pem
depends_on:
- beam-proxy
volumes:
- /tmp/bridgehead/opal-map/:/map/:ro
networks:
- default
- rstudio
traefik:
networks:
- default
- rstudio
forward_proxy:
networks:
- default
- rstudio
beam-proxy:
environment:
APP_datashield-connect_KEY: ${DATASHIELD_CONNECT_SECRET}
APP_token-manager_KEY: ${TOKEN_MANAGER_SECRET}
# TODO: Allow users of group /DataSHIELD and KEYCLOAK_USER_GROUP at the same time:
# Maybe a solution would be (https://oauth2-proxy.github.io/oauth2-proxy/docs/configuration/overview/):
# --allowed-groups=/DataSHIELD,KEYCLOAK_USER_GROUP
oauth2_proxy:
image: quay.io/oauth2-proxy/oauth2-proxy
container_name: bridgehead_oauth2_proxy
command: >-
--allowed-group=/DataSHIELD
--oidc-groups-claim=${KEYCLOAK_GROUP_CLAIM}
--auth-logging=true
--whitelist-domain=${HOST}
--http-address="0.0.0.0:4180"
--reverse-proxy=true
--upstream="static://202"
--email-domain="*"
--cookie-name="_BRIDGEHEAD_oauth2"
--cookie-secret="${OAUTH2_PROXY_SECRET}"
--cookie-expire="12h"
--cookie-secure="true"
--cookie-httponly="true"
#OIDC settings
--provider="keycloak-oidc"
--provider-display-name="VerbIS Login"
--client-id="${KEYCLOAK_PRIVATE_CLIENT_ID}"
--client-secret="${OIDC_CLIENT_SECRET}"
--redirect-url="https://${HOST}${OAUTH2_CALLBACK}"
--oidc-issuer-url="${KEYCLOAK_ISSUER_URL}"
--scope="openid email profile"
--code-challenge-method="S256"
--skip-provider-button=true
#X-Forwarded-Header settings - true/false depending on your needs
--pass-basic-auth=true
--pass-user-headers=false
--pass-access-token=false
labels:
- "traefik.enable=true"
- "traefik.http.routers.oauth2_proxy.rule=Host(`${HOST}`) && PathPrefix(`/oauth2`, `/oauth2/callback`)"
- "traefik.http.services.oauth2_proxy.loadbalancer.server.port=4180"
- "traefik.http.routers.oauth2_proxy.tls=true"
secrets:
opal-cert.pem:
file: /tmp/bridgehead/opal-cert.pem
opal-key.pem:
file: /tmp/bridgehead/opal-key.pem
networks:
rstudio:

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@ -1,157 +0,0 @@
<template id="opal-ccp" source-id="blaze-store" opal-project="ccp-demo" target-id="opal" >
<container csv-filename="Patient-${TIMESTAMP}.csv" opal-table="patient" opal-entity-type="Patient">
<attribute csv-column="patient-id" opal-value-type="text" primary-key="true" val-fhir-path="Patient.id.value" anonym="Pat" op="EXTRACT_RELATIVE_ID"/>
<attribute csv-column="dktk-id-global" opal-value-type="text" val-fhir-path="Patient.identifier.where(type.coding.code = 'Global').value.value"/>
<attribute csv-column="dktk-id-lokal" opal-value-type="text" val-fhir-path="Patient.identifier.where(type.coding.code = 'Lokal').value.value" />
<attribute csv-column="geburtsdatum" opal-value-type="date" val-fhir-path="Patient.birthDate.value"/>
<attribute csv-column="geschlecht" opal-value-type="text" val-fhir-path="Patient.gender.value" />
<attribute csv-column="datum_des_letztbekannten_vitalstatus" opal-value-type="date" val-fhir-path="Observation.where(code.coding.code = '75186-7').effective.value" join-fhir-path="/Observation.where(code.coding.code = '75186-7').subject.reference.value"/>
<attribute csv-column="vitalstatus" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '75186-7').value.coding.code.value" join-fhir-path="/Observation.where(code.coding.code = '75186-7').subject.reference.value"/>
<!--fehlt in ADT2FHIR--><attribute csv-column="tod_tumorbedingt" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '68343-3').value.coding.where(system = 'http://fhir.de/CodeSystem/bfarm/icd-10-gm').code.value" join-fhir-path="/Observation.where(code.coding.code = '68343-3').subject.reference.value"/>
<!--fehlt in ADT2FHIR--><attribute csv-column="todesursachen" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '68343-3').value.coding.where(system = 'http://dktk.dkfz.de/fhir/onco/core/CodeSystem/JNUCS').code.value" join-fhir-path="/Observation.where(code.coding.code = '68343-3').subject.reference.value"/>
</container>
<container csv-filename="Diagnosis-${TIMESTAMP}.csv" opal-table="diagnosis" opal-entity-type="Diagnosis">
<attribute csv-column="diagnosis-id" primary-key="true" opal-value-type="text" val-fhir-path="Condition.id.value" anonym="Dia" op="EXTRACT_RELATIVE_ID"/>
<attribute csv-column="patient-id" opal-value-type="text" val-fhir-path="Condition.subject.reference.value" anonym="Pat"/>
<attribute csv-column="primaerdiagnose" opal-value-type="text" val-fhir-path="Condition.code.coding.code.value"/>
<attribute csv-column="tumor_diagnosedatum" opal-value-type="date" val-fhir-path="Condition.onset.value"/>
<attribute csv-column="primaertumor_diagnosetext" opal-value-type="text" val-fhir-path="Condition.code.text.value"/>
<attribute csv-column="version_des_icd-10_katalogs" opal-value-type="integer" val-fhir-path="Condition.code.coding.version.value"/>
<attribute csv-column="lokalisation" opal-value-type="text" val-fhir-path="Condition.bodySite.coding.where(system = 'urn:oid:2.16.840.1.113883.6.43.1').code.value"/>
<attribute csv-column="icd-o_katalog_topographie_version" opal-value-type="text" val-fhir-path="Condition.bodySite.coding.where(system = 'urn:oid:2.16.840.1.113883.6.43.1').version.value"/>
<attribute csv-column="seitenlokalisation_nach_adt-gekid" opal-value-type="text" val-fhir-path="Condition.bodySite.coding.where(system = 'http://dktk.dkfz.de/fhir/onco/core/CodeSystem/SeitenlokalisationCS').code.value"/>
</container>
<container csv-filename="Progress-${TIMESTAMP}.csv" opal-table="progress" opal-entity-type="Progress">
<!--it would be better to generate a an ID, instead of extracting the ClinicalImpression id-->
<attribute csv-column="progress-id" primary-key="true" opal-value-type="text" val-fhir-path="ClinicalImpression.id.value" anonym="Pro" op="EXTRACT_RELATIVE_ID"/>
<attribute csv-column="diagnosis-id" opal-value-type="text" val-fhir-path="ClinicalImpression.problem.reference.value" anonym="Dia"/>
<attribute csv-column="patient-id" opal-value-type="text" val-fhir-path="ClinicalImpression.subject.reference.value" anonym="Pat" />
<attribute csv-column="untersuchungs-_befunddatum_im_verlauf" opal-value-type="date" val-fhir-path="ClinicalImpression.effective.value" />
<!-- just for evaluation: redundant to Untersuchungs-, Befunddatum im Verlauf-->
<attribute csv-column="datum_lokales_oder_regionaeres_rezidiv" opal-value-type="date" val-fhir-path="Observation.where(code.coding.code = 'LA4583-6').effective.value" join-fhir-path="ClinicalImpression.finding.itemReference.reference.value" />
<attribute csv-column="gesamtbeurteilung_tumorstatus" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '21976-6').value.coding.code.value" join-fhir-path="ClinicalImpression.finding.itemReference.reference.value"/>
<attribute csv-column="lokales_oder_regionaeres_rezidiv" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = 'LA4583-6').value.coding.code.value" join-fhir-path="ClinicalImpression.finding.itemReference.reference.value"/>
<attribute csv-column="lymphknoten-rezidiv" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = 'LA4370-8').value.coding.code.value" join-fhir-path="ClinicalImpression.finding.itemReference.reference.value" />
<attribute csv-column="fernmetastasen" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = 'LA4226-2').value.coding.code.value" join-fhir-path="ClinicalImpression.finding.itemReference.reference.value" />
</container>
<container csv-filename="Histology-${TIMESTAMP}.csv" opal-table="histology" opal-entity-type="Histology" >
<attribute csv-column="histology-id" primary-key="true" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '59847-4').id" anonym="His" op="EXTRACT_RELATIVE_ID"/>
<attribute csv-column="diagnosis-id" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '59847-4').focus.reference.value" anonym="Dia"/>
<attribute csv-column="patient-id" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '59847-4').subject.reference.value" anonym="Pat" />
<attribute csv-column="histologie_datum" opal-value-type="date" val-fhir-path="Observation.where(code.coding.code = '59847-4').effective.value"/>
<attribute csv-column="icd-o_katalog_morphologie_version" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '59847-4').value.coding.version.value" />
<attribute csv-column="morphologie" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '59847-4').value.coding.code.value"/>
<attribute csv-column="morphologie-freitext" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '59847-4').value.text.value"/>
<attribute csv-column="grading" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '59542-1').value.coding.code.value" join-fhir-path="Observation.where(code.coding.code = '59847-4').hasMember.reference.value"/>
</container>
<container csv-filename="Metastasis-${TIMESTAMP}.csv" opal-table="metastasis" opal-entity-type="Metastasis" >
<attribute csv-column="metastasis-id" primary-key="true" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '21907-1').id" anonym="Met" op="EXTRACT_RELATIVE_ID"/>
<attribute csv-column="diagnosis-id" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '21907-1').focus.reference.value" anonym="Dia"/>
<attribute csv-column="patient-id" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '21907-1').subject.reference.value" anonym="Pat" />
<attribute csv-column="datum_fernmetastasen" opal-value-type="date" val-fhir-path="Observation.where(code.coding.code = '21907-1').effective.value"/>
<attribute csv-column="fernmetastasen_vorhanden" opal-value-type="boolean" val-fhir-path="Observation.where(code.coding.code = '21907-1').value.coding.code.value"/>
<attribute csv-column="lokalisation_fernmetastasen" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '21907-1').bodySite.coding.code.value"/>
</container>
<container csv-filename="TNM-${TIMESTAMP}.csv" opal-table="tnm" opal-entity-type="TNM">
<attribute csv-column="tnm-id" primary-key="true" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '21908-9' or code.coding.code = '21902-2').id" anonym="TNM" op="EXTRACT_RELATIVE_ID"/>
<attribute csv-column="diagnosis-id" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '21908-9' or code.coding.code = '21902-2').focus.reference.value" anonym="Dia"/>
<attribute csv-column="patient-id" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '21908-9' or code.coding.code = '21902-2').subject.reference.value" anonym="Pat" />
<attribute csv-column="datum_der_tnm_dokumentation_datum_befund" opal-value-type="date" val-fhir-path="Observation.where(code.coding.code = '21908-9' or code.coding.code = '21902-2').effective.value"/>
<attribute csv-column="uicc_stadium" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '21908-9' or code.coding.code = '21902-2').value.coding.code.value"/>
<attribute csv-column="tnm-t" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '21908-9' or code.coding.code = '21902-2').component.where(code.coding.code = '21905-5' or code.coding.code = '21899-0').value.coding.code.value"/>
<attribute csv-column="tnm-n" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '21908-9' or code.coding.code = '21902-2').component.where(code.coding.code = '21906-3' or code.coding.code = '21900-6').value.coding.code.value"/>
<attribute csv-column="tnm-m" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '21908-9' or code.coding.code = '21902-2').component.where(code.coding.code = '21907-1' or code.coding.code = '21901-4').value.coding.code.value"/>
<attribute csv-column="c_p_u_preefix_t" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '21908-9' or code.coding.code = '21902-2').component.where(code.coding.code = '21905-5' or code.coding.code = '21899-0').extension('http://dktk.dkfz.de/fhir/StructureDefinition/onco-core-Extension-TNMcpuPraefix').value.coding.code.value"/>
<attribute csv-column="c_p_u_preefix_n" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '21908-9' or code.coding.code = '21902-2').component.where(code.coding.code = '21906-3' or code.coding.code = '21900-6').extension('http://dktk.dkfz.de/fhir/StructureDefinition/onco-core-Extension-TNMcpuPraefix').value.coding.code.value"/>
<attribute csv-column="c_p_u_preefix_m" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '21908-9' or code.coding.code = '21902-2').component.where(code.coding.code = '21907-1' or code.coding.code = '21901-4').extension('http://dktk.dkfz.de/fhir/StructureDefinition/onco-core-Extension-TNMcpuPraefix').value.coding.code.value"/>
<attribute csv-column="tnm-y-symbol" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '21908-9' or code.coding.code = '21902-2').component.where(code.coding.code = '59479-6' or code.coding.code = '59479-6').value.coding.code.value"/>
<attribute csv-column="tnm-r-symbol" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '21908-9' or code.coding.code = '21902-2').component.where(code.coding.code = '21983-2' or code.coding.code = '21983-2').value.coding.code.value"/>
<attribute csv-column="tnm-m-symbol" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '21908-9' or code.coding.code = '21902-2').component.where(code.coding.code = '42030-7' or code.coding.code = '42030-7').value.coding.code.value"/>
<!--nur bei UICC, nicht in ADT2FHIR--><attribute csv-column="tnm-version" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '21908-9' or code.coding.code = '21902-2').value.coding.version.value"/>
</container>
<container csv-filename="System-Therapy-${TIMESTAMP}.csv" opal-table="system-therapy" opal-entity-type="SystemTherapy">
<attribute csv-column="system-therapy-id" primary-key="true" opal-value-type="text" val-fhir-path="MedicationStatement.id" anonym="Sys" op="EXTRACT_RELATIVE_ID"/>
<attribute csv-column="diagnosis-id" opal-value-type="text" val-fhir-path="MedicationStatement.reasonReference.reference.value" anonym="Dia"/>
<attribute csv-column="patient-id" opal-value-type="text" val-fhir-path="MedicationStatement.subject.reference.value" anonym="Pat" />
<attribute csv-column="systemische_therapie_stellung_zu_operativer_therapie" opal-value-type="text" val-fhir-path="MedicationStatement.extension('http://dktk.dkfz.de/fhir/StructureDefinition/onco-core-Extension-StellungZurOp').value.coding.code.value"/>
<attribute csv-column="intention_chemotherapie" opal-value-type="text" val-fhir-path="MedicationStatement.extension('http://dktk.dkfz.de/fhir/StructureDefinition/onco-core-Extension-SYSTIntention').value.coding.code.value"/>
<attribute csv-column="therapieart" opal-value-type="text" val-fhir-path="MedicationStatement.category.coding.code.value"/>
<attribute csv-column="systemische_therapie_beginn" opal-value-type="date" val-fhir-path="MedicationStatement.effective.start.value"/>
<attribute csv-column="systemische_therapie_ende" opal-value-type="date" val-fhir-path="MedicationStatement.effective.end.value"/>
<attribute csv-column="systemische_therapie_protokoll" opal-value-type="text" val-fhir-path="MedicationStatement.extension('http://dktk.dkfz.de/fhir/StructureDefinition/onco-core-Extension-SystemischeTherapieProtokoll').value.text.value"/>
<attribute csv-column="systemische_therapie_substanzen" opal-value-type="text" val-fhir-path="MedicationStatement.medication.text.value"/>
<attribute csv-column="chemotherapie" opal-value-type="boolean" val-fhir-path="MedicationStatement.where(category.coding.code = 'CH').exists().value" />
<attribute csv-column="hormontherapie" opal-value-type="boolean" val-fhir-path="MedicationStatement.where(category.coding.code = 'HO').exists().value" />
<attribute csv-column="immuntherapie" opal-value-type="boolean" val-fhir-path="MedicationStatement.where(category.coding.code = 'IM').exists().value" />
<attribute csv-column="knochenmarktransplantation" opal-value-type="boolean" val-fhir-path="MedicationStatement.where(category.coding.code = 'KM').exists().value" />
<attribute csv-column="abwartende_strategie" opal-value-type="boolean" val-fhir-path="MedicationStatement.where(category.coding.code = 'WS').exists().value" />
</container>
<container csv-filename="Surgery-${TIMESTAMP}.csv" opal-table="surgery" opal-entity-type="Surgery">
<attribute csv-column="surgery-id" primary-key="true" opal-value-type="text" val-fhir-path="Procedure.where(category.coding.code = 'OP').id" anonym="Sur" op="EXTRACT_RELATIVE_ID"/>
<attribute csv-column="diagnosis-id" opal-value-type="text" val-fhir-path="Procedure.where(category.coding.code = 'OP').reasonReference.reference.value" anonym="Dia"/>
<attribute csv-column="patient-id" opal-value-type="text" val-fhir-path="Procedure.where(category.coding.code = 'OP').subject.reference.value" anonym="Pat" />
<attribute csv-column="ops-code" opal-value-type="text" val-fhir-path="Procedure.where(category.coding.code = 'OP').code.coding.code.value"/>
<attribute csv-column="datum_der_op" opal-value-type="date" val-fhir-path="Procedure.where(category.coding.code = 'OP').performed.value"/>
<attribute csv-column="intention_op" opal-value-type="text" val-fhir-path="Procedure.extension('http://dktk.dkfz.de/fhir/StructureDefinition/onco-core-Extension-OPIntention').value.coding.code.value"/>
<attribute csv-column="lokale_beurteilung_resttumor" opal-value-type="text" val-fhir-path="Procedure.where(category.coding.code = 'OP').outcome.coding.where(system = 'http://dktk.dkfz.de/fhir/onco/core/CodeSystem/LokaleBeurteilungResidualstatusCS').code.value" />
<attribute csv-column="gesamtbeurteilung_resttumor" opal-value-type="text" val-fhir-path="Procedure.where(category.coding.code = 'OP').outcome.coding.where(system = 'http://dktk.dkfz.de/fhir/onco/core/CodeSystem/GesamtbeurteilungResidualstatusCS').code.value" />
</container>
<container csv-filename="Radiation-Therapy-${TIMESTAMP}.csv" opal-table="radiation-therapy" opal-entity-type="RadiationTherapy">
<attribute csv-column="radiation-therapy-id" primary-key="true" opal-value-type="text" val-fhir-path="Procedure.where(category.coding.code = 'ST').id" anonym="Rad" op="EXTRACT_RELATIVE_ID"/>
<attribute csv-column="diagnosis-id" opal-value-type="text" val-fhir-path="Procedure.where(category.coding.code = 'ST').reasonReference.reference.value" anonym="Dia"/>
<attribute csv-column="patient-id" opal-value-type="text" val-fhir-path="Procedure.where(category.coding.code = 'ST').subject.reference.value" anonym="Pat" />
<attribute csv-column="strahlentherapie_stellung_zu_operativer_therapie" opal-value-type="text" val-fhir-path="Procedure.extension('http://dktk.dkfz.de/fhir/StructureDefinition/onco-core-Extension-StellungZurOp').value.coding.code.value"/>
<attribute csv-column="intention_strahlentherapie" opal-value-type="text" val-fhir-path="Procedure.extension('http://dktk.dkfz.de/fhir/StructureDefinition/onco-core-Extension-SYSTIntention').value.coding.code.value" />
<attribute csv-column="strahlentherapie_beginn" opal-value-type="date" val-fhir-path="Procedure.where(category.coding.code = 'ST').performed.start.value"/>
<attribute csv-column="strahlentherapie_ende" opal-value-type="date" val-fhir-path="Procedure.where(category.coding.code = 'ST').performed.end.value"/>
</container>
<container csv-filename="Molecular-Marker-${TIMESTAMP}.csv" opal-table="molecular-marker" opal-entity-type="MolecularMarker">
<attribute csv-column="mol-marker-id" primary-key="true" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '69548-6').id" anonym="Mol" op="EXTRACT_RELATIVE_ID"/>
<attribute csv-column="diagnosis-id" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '69548-6').focus.reference.value" anonym="Dia" />
<attribute csv-column="patient-id" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '69548-6').subject.reference.value" anonym="Pat" />
<attribute csv-column="datum_der_datenerhebung" opal-value-type="date" val-fhir-path="Observation.where(code.coding.code = '69548-6').effective.value"/>
<attribute csv-column="marker" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '69548-6').component.value.coding.code.value"/>
<attribute csv-column="status_des_molekularen_markers" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '69548-6').value.coding.code.value" />
<attribute csv-column="zusaetzliche_alternative_dokumentation" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '69548-6').value.text.value"/>
</container>
<container csv-filename="Sample-${TIMESTAMP}.csv" opal-table="sample" opal-entity-type="Sample">
<attribute csv-column="sample-id" primary-key="true" opal-value-type="text" val-fhir-path="Specimen.id" anonym="Sam" op="EXTRACT_RELATIVE_ID"/>
<attribute csv-column="patient-id" opal-value-type="text" val-fhir-path="Specimen.subject.reference.value" anonym="Pat" />
<attribute csv-column="entnahmedatum" opal-value-type="date" val-fhir-path="Specimen.collection.collectedDateTime.value"/>
<attribute csv-column="probenart" opal-value-type="text" val-fhir-path="Specimen.type.coding.code.value"/>
<attribute csv-column="status" opal-value-type="text" val-fhir-path="Specimen.status.code.value"/>
<attribute csv-column="projekt" opal-value-type="text" val-fhir-path="Specimen.identifier.system.value"/>
<!-- @TODO: it is still necessary to clarify whether it would not be better to take the quantity of collection.quantity -->
<attribute csv-column="menge" opal-value-type="integer" val-fhir-path="Specimen.container.specimenQuantity.value.value"/>
<attribute csv-column="einheit" opal-value-type="text" val-fhir-path="Specimen.container.specimenQuantity.unit.value"/>
<attribute csv-column="aliquot" opal-value-type="text" val-fhir-path="Specimen.parent.reference.exists().value" />
</container>
<fhir-rev-include>Observation:patient</fhir-rev-include>
<fhir-rev-include>Condition:patient</fhir-rev-include>
<fhir-rev-include>ClinicalImpression:patient</fhir-rev-include>
<fhir-rev-include>MedicationStatement:patient</fhir-rev-include>
<fhir-rev-include>Procedure:patient</fhir-rev-include>
<fhir-rev-include>Specimen:patient</fhir-rev-include>
</template>

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@ -1,13 +0,0 @@
[
"berlin",
"muenchen-lmu",
"dresden",
"freiburg",
"muenchen-tum",
"tuebingen",
"mainz",
"frankfurt",
"essen",
"dktk-datashield-test",
"dktk-test"
]

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@ -1,33 +0,0 @@
#!/bin/bash -e
if [ "$ENABLE_DATASHIELD" == true ]; then
log INFO "DataSHIELD setup detected -- will start DataSHIELD services."
OVERRIDE+=" -f ./$PROJECT/modules/datashield-compose.yml"
EXPORTER_OPAL_PASSWORD="$(generate_password \"exporter in Opal\")"
TOKEN_MANAGER_OPAL_PASSWORD="$(generate_password \"Token Manager in Opal\")"
OPAL_DB_PASSWORD="$(echo \"Opal DB\" | generate_simple_password)"
OPAL_ADMIN_PASSWORD="$(generate_password \"admin password for Opal\")"
RSTUDIO_ADMIN_PASSWORD="$(generate_password \"admin password for R-Studio\")"
DATASHIELD_CONNECT_SECRET="$(echo \"DataShield Connect\" | generate_simple_password)"
TOKEN_MANAGER_SECRET="$(echo \"Token Manager\" | generate_simple_password)"
if [ ! -e /tmp/bridgehead/opal-cert.pem ]; then
mkdir -p /tmp/bridgehead/
chown -R bridgehead:docker /tmp/bridgehead/
openssl req -x509 -newkey rsa:4096 -nodes -keyout /tmp/bridgehead/opal-key.pem -out /tmp/bridgehead/opal-cert.pem -days 3650 -subj "/CN=opal/C=DE"
chmod g+r /tmp/bridgehead/opal-key.pem
fi
mkdir -p /tmp/bridgehead/opal-map
jq -n '{"sites": input | map({
"name": .,
"id": .,
"virtualhost": "\(.):443",
"beamconnect": "datashield-connect.\(.).'"$BROKER_ID"'"
})}' ./$PROJECT/modules/datashield-mappings.json > /tmp/bridgehead/opal-map/central.json
jq -n '[{
"external": "'"$SITE_ID"':443",
"internal": "opal:8443",
"allowed": input | map("datashield-connect.\(.).'"$BROKER_ID"'")
}]' ./$PROJECT/modules/datashield-mappings.json > /tmp/bridgehead/opal-map/local.json
chown -R bridgehead:docker /tmp/bridgehead/
add_private_oidc_redirect_url "/opal/*"
fi

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@ -1,28 +0,0 @@
# DataSHIELD
This module constitutes the infrastructure to run DataSHIELD within the bridghead.
For more information about DataSHIELD, please visit https://www.datashield.org/
## R-Studio
To connect to the different bridgeheads of the CCP through DataSHIELD, you can use your own R-Studio environment.
However, this R-Studio has already installed the DataSHIELD libraries and is integrated within the bridgehead.
This can save you some time for extra configuration of your R-Studio environment.
## Opal
This is the core of DataSHIELD. It is made up of Opal, a Postgres database and an R-server.
For more information about Opal, please visit https://opaldoc.obiba.org
### Opal
Opal is OBiBas core database application for biobanks.
### Opal-DB
Opal requires a database to import the data for DataSHIELD. We use a Postgres instance as database.
The data is imported within the bridgehead through the exporter.
### Opal-R-Server
R-Server to execute R scripts in DataSHIELD.
## Beam
### Beam-Connect
Beam-Connect is used to route http(s) traffic through beam to enable R-Studio to access data from other bridgeheads that have datashield enabled.
### Beam-Proxy
The usual beam proxy used for communication.

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@ -16,12 +16,14 @@ services:
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
NO_PROXY: beam-proxy,dnpm-backend,host.docker.internal${DNPM_ADDITIONAL_NO_PROXY}
RUST_LOG: ${RUST_LOG:-info}
NO_AUTH: "true"
TLS_CA_CERTIFICATES_DIR: ./conf/trusted-ca-certs
extra_hosts:
- "host.docker.internal:host-gateway"
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
labels:
@ -31,3 +33,7 @@ services:
- "traefik.http.routers.dnpm-connect.middlewares=dnpm-connect-strip"
- "traefik.http.services.dnpm-connect.loadbalancer.server.port=8062"
- "traefik.http.routers.dnpm-connect.tls=true"
dnpm-echo:
image: docker.verbis.dkfz.de/cache/samply/bridgehead-echo:latest
container_name: bridgehead-dnpm-echo

View File

@ -6,6 +6,7 @@ services:
container_name: bridgehead-dnpm-backend
environment:
- ZPM_SITE=${ZPM_SITE}
- N_RANDOM_FILES=${DNPM_SYNTH_NUM}
volumes:
- /etc/bridgehead/dnpm:/bwhc_config:ro
- ${DNPM_DATA_DIR}:/bwhc_data

View File

@ -14,14 +14,15 @@ if [ -n "${ENABLE_DNPM_NODE}" ]; then
log ERROR "Mandatory variable DNPM_DATA_DIR not defined!"
exit 1
fi
if grep -q 'traefik.http.routers.landing.rule=PathPrefix(`/landing`)' /srv/docker/bridgehead/minimal/docker-compose.override.yml 2>/dev/null; then
echo "Override of landing page url already in place"
else
echo "Adding override of landing page url"
if [ -f /srv/docker/bridgehead/minimal/docker-compose.override.yml ]; then
echo -e ' landing:\n labels:\n - "traefik.http.routers.landing.rule=PathPrefix(`/landing`)"' >> /srv/docker/bridgehead/minimal/docker-compose.override.yml
else
echo -e 'version: "3.7"\nservices:\n landing:\n labels:\n - "traefik.http.routers.landing.rule=PathPrefix(`/landing`)"' >> /srv/docker/bridgehead/minimal/docker-compose.override.yml
fi
fi
DNPM_SYNTH_NUM=${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
fi

View File

@ -1,4 +1,4 @@
#!/bin/bash -e
#!/bin/bash
if [ -n "${ENABLE_DNPM}" ]; then
log INFO "DNPM setup detected (Beam.Connect) -- will start Beam.Connect for DNPM."
@ -6,4 +6,10 @@ if [ -n "${ENABLE_DNPM}" ]; then
# Set variables required for Beam-Connect
DNPM_BEAM_SECRET_SHORT="$(cat /proc/sys/kernel/random/uuid | sed 's/[-]//g' | head -c 20)"
# If the DNPM_NO_PROXY variable is set, prefix it with a comma (as it gets added to a comma separated list)
if [ -n "${DNPM_NO_PROXY}" ]; then
DNPM_ADDITIONAL_NO_PROXY=",${DNPM_NO_PROXY}"
else
DNPM_ADDITIONAL_NO_PROXY=""
fi
fi

View File

@ -1,6 +0,0 @@
# Full Excel Export
curl --location --request POST 'https://${HOST}/ccp-exporter/request?query=Patient&query-format=FHIR_PATH&template-id=ccp&output-format=EXCEL' \
--header 'x-api-key: ${EXPORT_API_KEY}'
# QB
curl --location --request POST 'https://${HOST}/ccp-reporter/generate?template-id=ccp'

View File

@ -1,67 +0,0 @@
version: "3.7"
services:
exporter:
image: docker.verbis.dkfz.de/ccp/dktk-exporter:latest
container_name: bridgehead-ccp-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: "${EXPORTER_DB_PASSWORD}" # Set in exporter-setup.sh
EXPORTER_DB_URL: "jdbc:postgresql://exporter-db:5432/exporter"
HTTP_RELATIVE_PATH: "/ccp-exporter"
SITE: "${SITE_ID}"
HTTP_SERVLET_REQUEST_SCHEME: "https"
OPAL_PASSWORD: "${EXPORTER_OPAL_PASSWORD}"
labels:
- "traefik.enable=true"
- "traefik.http.routers.exporter_ccp.rule=PathPrefix(`/ccp-exporter`)"
- "traefik.http.services.exporter_ccp.loadbalancer.server.port=8092"
- "traefik.http.routers.exporter_ccp.tls=true"
- "traefik.http.middlewares.exporter_ccp_strip.stripprefix.prefixes=/ccp-exporter"
- "traefik.http.routers.exporter_ccp.middlewares=exporter_ccp_strip"
volumes:
- "/var/cache/bridgehead/ccp/exporter-files:/app/exporter-files/output"
exporter-db:
image: docker.verbis.dkfz.de/cache/postgres:15.4-alpine
container_name: bridgehead-ccp-exporter-db
environment:
POSTGRES_USER: "exporter"
POSTGRES_PASSWORD: "${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"
reporter:
image: docker.verbis.dkfz.de/ccp/dktk-reporter:latest
container_name: bridgehead-ccp-reporter
environment:
JAVA_OPTS: "-Xms1G -Xmx8G -XX:+UseG1GC"
LOG_LEVEL: "INFO"
CROSS_ORIGINS: "https://${HOST}"
HTTP_RELATIVE_PATH: "/ccp-reporter"
SITE: "${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/ccp/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"

View File

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

View File

@ -1,15 +0,0 @@
# Exporter and Reporter
## Exporter
The exporter is a REST API that exports the data of the different databases of the bridgehead in a set of tables.
It can accept different output formats as CSV, Excel, JSON or XML. It can also export data into Opal.
## Exporter-DB
It is a database to save queries for its execution in the exporter.
The exporter manages also the different executions of the same query in through the database.
## Reporter
This component is a plugin of the exporter that allows to create more complex Excel reports described in templates.
It is compatible with different template engines as Groovy, Thymeleaf,...
It is perfect to generate a document as our traditional CCP quality report.

View File

@ -1,5 +1,4 @@
version: "3.7"
services:
id-manager:
image: docker.verbis.dkfz.de/bridgehead/magicpl

View File

@ -1,4 +1,4 @@
#!/bin/bash -e
#!/bin/bash
function idManagementSetup() {
if [ -n "$IDMANAGER_UPLOAD_APIKEY" ]; then

View File

@ -1,47 +0,0 @@
version: "3.7"
services:
login-db:
image: docker.verbis.dkfz.de/cache/postgres:15.4-alpine
container_name: bridgehead-login-db
environment:
POSTGRES_USER: "keycloak"
POSTGRES_PASSWORD: "${KEYCLOAK_DB_PASSWORD}" # Set in login-setup.sh
POSTGRES_DB: "keycloak"
tmpfs:
- /var/lib/postgresql/data
# Consider removing this comment once we have collected experience in production.
# volumes:
# - "bridgehead-login-db:/var/lib/postgresql/data"
login:
image: docker.verbis.dkfz.de/ccp/dktk-keycloak:latest
container_name: bridgehead-login
environment:
KEYCLOAK_ADMIN: "admin"
KEYCLOAK_ADMIN_PASSWORD: "${LDM_AUTH}"
TEILER_ADMIN: "${PROJECT}"
TEILER_ADMIN_PASSWORD: "${LDM_AUTH}"
TEILER_ADMIN_FIRST_NAME: "${OPERATOR_FIRST_NAME}"
TEILER_ADMIN_LAST_NAME: "${OPERATOR_LAST_NAME}"
TEILER_ADMIN_EMAIL: "${OPERATOR_EMAIL}"
KC_DB_PASSWORD: "${KEYCLOAK_DB_PASSWORD}" # Set in login-setup.sh
KC_HOSTNAME_URL: "https://${HOST}/login"
KC_HOSTNAME_STRICT: "false"
KC_PROXY_ADDRESS_FORWARDING: "true"
TEILER_ORCHESTRATOR_EXTERN_URL: "https://${HOST}/ccp-teiler"
command:
- start-dev --import-realm --proxy edge --http-relative-path=/login
labels:
- "traefik.enable=true"
- "traefik.http.routers.login.rule=PathPrefix(`/login`)"
- "traefik.http.services.login.loadbalancer.server.port=8080"
- "traefik.http.routers.login.tls=true"
depends_on:
- login-db
# Consider removing this comment once we have collected experience in production.
#volumes:
# bridgehead-login-db:
# name: "bridgehead-login-db"

View File

@ -1,7 +0,0 @@
#!/bin/bash -e
if [ "$ENABLE_LOGIN" == true ]; then
log INFO "Login setup detected -- will start Login services."
OVERRIDE+=" -f ./$PROJECT/modules/login-compose.yml"
KEYCLOAK_DB_PASSWORD="$(generate_password \"local Keycloak\")"
fi

View File

@ -1,13 +0,0 @@
# Login
The login component is a local Keycloak instance. In the future will be replaced by the central keycloak instance
or maybe can be used to add local identity providers to the bridgehead or just to simplify the configuration of
the central keycloak instance for the integration of every new bridgehead.
The basic configuration of our Keycloak instance is contained in a small json file.
### Teiler User
Currently, the local keycloak is used by the teiler. There is a basic admin user in the basic configuration of keycloak.
The user can be configured with the environment variables TEILER_ADMIN_XXX.
## Login-DB
Keycloak requires a local database for its configuration. However, as we use an initial json configuration file, if no
local identity provider is configured nor any local user, theoretically we don't need a volume for the login.

View File

@ -2,8 +2,7 @@ version: "3.7"
services:
mtba:
#image: docker.verbis.dkfz.de/cache/samply/mtba:latest
image: docker.verbis.dkfz.de/cache/samply/mtba:develop
image: docker.verbis.dkfz.de/cache/samply/mtba:1.0.0
container_name: bridgehead-mtba
environment:
BLAZE_STORE_URL: http://blaze:8080
@ -12,30 +11,22 @@ services:
ID_MANAGER_API_KEY: ${IDMANAGER_UPLOAD_APIKEY}
ID_MANAGER_PSEUDONYM_ID_TYPE: BK_${IDMANAGEMENT_FRIENDLY_ID}_L-ID
ID_MANAGER_URL: http://id-manager:8080/id-manager
PATIENT_CSV_FIRST_NAME_HEADER: ${MTBA_PATIENT_CSV_FIRST_NAME_HEADER:-FIRST_NAME}
PATIENT_CSV_LAST_NAME_HEADER: ${MTBA_PATIENT_CSV_LAST_NAME_HEADER:-LAST_NAME}
PATIENT_CSV_GENDER_HEADER: ${MTBA_PATIENT_CSV_GENDER_HEADER:-GENDER}
PATIENT_CSV_BIRTHDAY_HEADER: ${MTBA_PATIENT_CSV_BIRTHDAY_HEADER:-BIRTHDAY}
PATIENT_CSV_FIRST_NAME_HEADER: ${MTBA_PATIENT_CSV_FIRST_NAME_HEADER}
PATIENT_CSV_LAST_NAME_HEADER: ${MTBA_PATIENT_CSV_LAST_NAME_HEADER}
PATIENT_CSV_GENDER_HEADER: ${MTBA_PATIENT_CSV_GENDER_HEADER}
PATIENT_CSV_BIRTHDAY_HEADER: ${MTBA_PATIENT_CSV_BIRTHDAY_HEADER}
CBIOPORTAL_URL: http://cbioportal:8080
FILE_CHARSET: ${MTBA_FILE_CHARSET:-UTF-8}
FILE_END_OF_LINE: ${MTBA_FILE_END_OF_LINE:-LF}
CSV_DELIMITER: ${MTBA_CSV_DELIMITER:-TAB}
HTTP_RELATIVE_PATH: "/mtba"
KEYCLOAK_ADMIN_GROUP: "${KEYCLOAK_ADMIN_GROUP}"
KEYCLOAK_CLIENT_ID: "${KEYCLOAK_PRIVATE_CLIENT_ID}"
KEYCLOAK_CLIENT_SECRET: "${OIDC_CLIENT_SECRET}"
KEYCLOAK_REALM: "${KEYCLOAK_REALM}"
KEYCLOAK_URL: "${KEYCLOAK_URL}"
FILE_CHARSET: ${MTBA_FILE_CHARSET}
FILE_END_OF_LINE: ${MTBA_FILE_END_OF_LINE}
CSV_DELIMITER: ${MTBA_CSV_DELIMITER}
labels:
- "traefik.enable=true"
- "traefik.http.routers.mtba_ccp.rule=PathPrefix(`/mtba`)"
- "traefik.http.services.mtba_ccp.loadbalancer.server.port=8480"
- "traefik.http.routers.mtba_ccp.tls=true"
- "traefik.http.routers.mtba.rule=PathPrefix(`/`)"
- "traefik.http.services.mtba.loadbalancer.server.port=80"
- "traefik.http.routers.mtba.tls=true"
volumes:
- /var/cache/bridgehead/ccp/mtba/input:/app/input
- /var/cache/bridgehead/ccp/mtba/persist:/app/persist
- /tmp/bridgehead/mtba/input:/app/input
- /tmp/bridgehead/mtba/persist:/app/persist
# TODO: Include CBioPortal in Deployment ...
# NOTE: CBioPortal can't load data while the system is running. So after import of data bridgehead needs to be restarted!

View File

@ -1,4 +1,4 @@
#!/bin/bash -e
#!/bin/bash
function mtbaSetup() {
if [ -n "$ENABLE_MTBA" ];then
@ -8,6 +8,5 @@ function mtbaSetup() {
exit 1;
fi
OVERRIDE+=" -f ./$PROJECT/modules/mtba-compose.yml"
add_private_oidc_redirect_url "/mtba/*"
fi
}
}

View File

@ -1,6 +0,0 @@
# Molecular Tumor Board Alliance (MTBA)
In this module, the genetic data to import is stored in a directory (/tmp/bridgehead/mtba/input). A process checks
regularly if there are files in the directory. The files are pseudonomized when the IDAT is provided. The files are
combined with clinical data of the blaze and imported in cBioPortal. On the other hand, this files are also imported in
Blaze.

View File

@ -1,5 +1,4 @@
version: "3.7"
volumes:
nngm-rest:
@ -22,6 +21,9 @@ services:
- "traefik.http.routers.connector.middlewares=connector_strip,auth-nngm"
volumes:
- nngm-rest:/var/log
traefik:
labels:
- "traefik.http.middlewares.auth-nngm.basicauth.users=${NNGM_AUTH}"

View File

@ -1,4 +1,4 @@
#!/bin/bash -e
#!/bin/bash
if [ -n "$NNGM_CTS_APIKEY" ]; then
log INFO "nNGM setup detected -- will start nNGM Connector."

View File

@ -1,82 +0,0 @@
version: "3.7"
services:
teiler-orchestrator:
image: docker.verbis.dkfz.de/cache/samply/teiler-orchestrator:latest
container_name: bridgehead-teiler-orchestrator
labels:
- "traefik.enable=true"
- "traefik.http.routers.teiler_orchestrator_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"
environment:
TEILER_BACKEND_URL: "https://${HOST}/ccp-teiler-backend"
TEILER_DASHBOARD_URL: "https://${HOST}/ccp-teiler-dashboard"
DEFAULT_LANGUAGE: "${DEFAULT_LANGUAGE_LOWER_CASE}"
HTTP_RELATIVE_PATH: "/ccp-teiler"
teiler-dashboard:
image: docker.verbis.dkfz.de/cache/samply/teiler-dashboard:latest
container_name: bridgehead-teiler-dashboard
labels:
- "traefik.enable=true"
- "traefik.http.routers.teiler_dashboard_ccp.rule=PathPrefix(`/ccp-teiler-dashboard`)"
- "traefik.http.services.teiler_dashboard_ccp.loadbalancer.server.port=80"
- "traefik.http.routers.teiler_dashboard_ccp.tls=true"
- "traefik.http.middlewares.teiler_dashboard_ccp_strip.stripprefix.prefixes=/ccp-teiler-dashboard"
- "traefik.http.routers.teiler_dashboard_ccp.middlewares=teiler_dashboard_ccp_strip"
environment:
DEFAULT_LANGUAGE: "${DEFAULT_LANGUAGE}"
TEILER_BACKEND_URL: "https://${HOST}/ccp-teiler-backend"
KEYCLOAK_URL: "${KEYCLOAK_URL}"
KEYCLOAK_REALM: "${KEYCLOAK_REALM}"
KEYCLOAK_CLIENT_ID: "${KEYCLOAK_PUBLIC_CLIENT_ID}"
KEYCLOAK_TOKEN_GROUP: "${KEYCLOAK_GROUP_CLAIM}"
TEILER_ADMIN_NAME: "${OPERATOR_FIRST_NAME} ${OPERATOR_LAST_NAME}"
TEILER_ADMIN_EMAIL: "${OPERATOR_EMAIL}"
TEILER_ADMIN_PHONE: "${OPERATOR_PHONE}"
TEILER_PROJECT: "${PROJECT}"
EXPORTER_API_KEY: "${EXPORTER_API_KEY}"
TEILER_ORCHESTRATOR_URL: "https://${HOST}/ccp-teiler"
TEILER_DASHBOARD_HTTP_RELATIVE_PATH: "/ccp-teiler-dashboard"
TEILER_ORCHESTRATOR_HTTP_RELATIVE_PATH: "/ccp-teiler"
TEILER_USER: "${KEYCLOAK_USER_GROUP}"
TEILER_ADMIN: "${KEYCLOAK_ADMIN_GROUP}"
REPORTER_DEFAULT_TEMPLATE_ID: "ccp-qb"
EXPORTER_DEFAULT_TEMPLATE_ID: "ccp"
teiler-backend:
# image: docker.verbis.dkfz.de/ccp/dktk-teiler-backend:latest
image: dktk-teiler-backend
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"
environment:
LOG_LEVEL: "INFO"
APPLICATION_PORT: "8085"
APPLICATION_ADDRESS: "${HOST}"
DEFAULT_LANGUAGE: "${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}"
secrets:
- ccp.conf
secrets:
ccp.conf:
file: /etc/bridgehead/ccp.conf

View File

@ -1,7 +0,0 @@
#!/bin/bash -e
if [ "$ENABLE_TEILER" == true ];then
log INFO "Teiler setup detected -- will start Teiler services."
OVERRIDE+=" -f ./$PROJECT/modules/teiler-compose.yml"
add_public_oidc_redirect_url "/ccp-teiler/*"
fi

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@ -1,19 +0,0 @@
# Teiler
This module orchestrates the different microfrontends of the bridgehead as a single page application.
## Teiler Orchestrator
Single SPA component that consists on the root HTML site of the single page application and a javascript code that
gets the information about the microfrontend calling the teiler backend and is responsible for registering them. With the
resulting mapping, it can initialize, mount and unmount the required microfrontends on the fly.
The microfrontends run independently in different containers and can be based on different frameworks (Angular, Vue, React,...)
This microfrontends can run as single alone but need an extension with Single-SPA (https://single-spa.js.org/docs/ecosystem).
There are also available three templates (Angular, Vue, React) to be directly extended to be used directly in the teiler.
## Teiler Dashboard
It consists on the main dashboard and a set of embedded services.
### Login
user and password in ccp.local.conf
## Teiler Backend
In this component, the microfrontends are configured.

View File

@ -7,25 +7,7 @@ SUPPORT_EMAIL=support-ccp@dkfz-heidelberg.de
PRIVATEKEYFILENAME=/etc/bridgehead/pki/${SITE_ID}.priv.pem
BROKER_URL_FOR_PREREQ=$BROKER_URL
DEFAULT_LANGUAGE=DE
DEFAULT_LANGUAGE_LOWER_CASE=${DEFAULT_LANGUAGE,,}
ENABLE_EXPORTER=true
ENABLE_TEILER=true
#ENABLE_DATASHIELD=true
KEYCLOAK_USER_GROUP="DKTK_CCP_$(capitalize_first_letter ${SITE_ID})"
KEYCLOAK_ADMIN_GROUP="DKTK_CCP_$(capitalize_first_letter ${SITE_ID})_Verwalter"
KEYCLOAK_PRIVATE_CLIENT_ID=${SITE_ID}-private
KEYCLOAK_PUBLIC_CLIENT_ID=${SITE_ID}-public
# TODO: Change Keycloak Realm to productive. "test-realm-01" is only for testing
KEYCLOAK_REALM="${KEYCLOAK_REALM:-test-realm-01}"
KEYCLOAK_URL="https://login.verbis.dkfz.de"
KEYCLOAK_ISSUER_URL="${KEYCLOAK_URL}/realms/${KEYCLOAK_REALM}"
KEYCLOAK_GROUP_CLAIM="groups"
OAUTH2_CALLBACK=/oauth2/callback
OAUTH2_PROXY_SECRET="$(echo \"This is a salt string to generate one consistent encryption key for the oauth2_proxy. It is not required to be secret.\" | openssl rsautl -sign -inkey /etc/bridgehead/pki/${SITE_ID}.priv.pem | base64 | head -c 32)"
add_private_oidc_redirect_url "${OAUTH2_CALLBACK}"
for module in $PROJECT/modules/*.sh
do
@ -35,4 +17,4 @@ done
idManagementSetup
mtbaSetup
adt2fhirRestSetup
adt2fhirRestSetup

View File

@ -53,7 +53,7 @@ checkOwner(){
}
printUsage() {
echo "Usage: bridgehead start|stop|is-running|update|install|uninstall|adduser|enroll PROJECTNAME"
echo "Usage: bridgehead start|stop|logs|is-running|update|install|uninstall|adduser|enroll PROJECTNAME"
echo "PROJECTNAME should be one of ccp|bbmri"
}
@ -239,109 +239,3 @@ add_basic_auth_user() {
log DEBUG "Saving clear text credentials in $FILE. If wanted, delete them manually."
sed -i "/^$NAME/ s|$|\n# User: $USER\n# Password: $PASSWORD|" $FILE
}
OIDC_PUBLIC_REDIRECT_URLS=${OIDC_PUBLIC_REDIRECT_URLS:-""}
OIDC_PRIVATE_REDIRECT_URLS=${OIDC_PRIVATE_REDIRECT_URLS:-""}
# Add a redirect url to the public oidc client of the bridgehead
function add_public_oidc_redirect_url() {
if [[ $OIDC_PUBLIC_REDIRECT_URLS == "" ]]; then
OIDC_PUBLIC_REDIRECT_URLS+="$(generate_redirect_urls $1)"
else
OIDC_PUBLIC_REDIRECT_URLS+=",$(generate_redirect_urls $1)"
fi
}
# Add a redirect url to the private oidc client of the bridgehead
function add_private_oidc_redirect_url() {
if [[ $OIDC_PRIVATE_REDIRECT_URLS == "" ]]; then
OIDC_PRIVATE_REDIRECT_URLS+="$(generate_redirect_urls $1)"
else
OIDC_PRIVATE_REDIRECT_URLS+=",$(generate_redirect_urls $1)"
fi
}
function sync_secrets() {
local delimiter=$'\x1E'
local secret_sync_args=""
if [[ $OIDC_PRIVATE_REDIRECT_URLS != "" ]]; then
secret_sync_args="OIDC:OIDC_CLIENT_SECRET:private;$OIDC_PRIVATE_REDIRECT_URLS"
fi
if [[ $OIDC_PRIVATE_REDIRECT_URLS != "" ]]; then
if [[ $secret_sync_args == "" ]]; then
secret_sync_args="OIDC:OIDC_PUBLIC:public;$OIDC_PUBLIC_REDIRECT_URLS"
else
secret_sync_args+="${delimiter}OIDC:OIDC_PUBLIC:public;$OIDC_PUBLIC_REDIRECT_URLS"
fi
fi
if [[ $secret_sync_args == "" ]]; then
return
fi
mkdir -p /var/cache/bridgehead/secrets/
touch /var/cache/bridgehead/secrets/oidc
chown -R bridgehead:docker /var/cache/bridgehead/secrets
# The oidc provider will need to be switched based on the project at some point I guess
docker run --rm \
-v /var/cache/bridgehead/secrets/oidc:/usr/local/cache \
-v $PRIVATEKEYFILENAME:/run/secrets/privkey.pem:ro \
-v /srv/docker/bridgehead/$PROJECT/root.crt.pem:/run/secrets/root.crt.pem:ro \
-v /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro \
-e TLS_CA_CERTIFICATES_DIR=/conf/trusted-ca-certs \
-e HTTPS_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 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/*
set +a # Export variables in the regular way
}
capitalize_first_letter() {
input="$1"
capitalized="$(tr '[:lower:]' '[:upper:]' <<< ${input:0:1})${input:1}"
echo "$capitalized"
}
# Generate a string of ',' separated string of redirect urls relative to $HOST.
# $1 will be appended to the url
# If the host looks like dev-jan.inet.dkfz-heidelberg.de it will generate urls with dev-jan and the original $HOST as url Authorities
function generate_redirect_urls(){
local redirect_urls="https://${HOST}$1"
local host_without_proxy="$(echo "$HOST" | cut -d '.' -f1)"
# Only append second url if its different and the host is not an ip address
if [[ "$HOST" != "$host_without_proxy" && ! "$HOST" =~ ^[0-9]+\.[0-9]+\.[0-9]+\.[0-9]+$ ]]; then
redirect_urls+=",https://$host_without_proxy$1"
fi
echo "$redirect_urls"
}
# This password contains at least one special char, a random number and a random upper and lower case letter
generate_password(){
local seed_text="$1"
local seed_num=$(awk 'BEGIN{FS=""} NR==1{print $10}' /etc/bridgehead/pki/${SITE_ID}.priv.pem | od -An -tuC)
local nums="1234567890"
local n=$(echo "$seed_num" | awk '{print $1 % 10}')
local random_digit=${nums:$n:1}
local n=$(echo "$seed_num" | awk '{print $1 % 26}')
local upper="ABCDEFGHIJKLMNOPQRSTUVWXYZ"
local lower="abcdefghijklmnopqrstuvwxyz"
local random_upper=${upper:$n:1}
local random_lower=${lower:$n:1}
local n=$(echo "$seed_num" | awk '{print $1 % 8}')
local special='@#$%^&+='
local random_special=${special:$n:1}
local combined_text="This is a salt string to generate one consistent password for ${seed_text}. It is not required to be secret."
local main_password=$(echo "${combined_text}" | openssl rsautl -sign -inkey "/etc/bridgehead/pki/${SITE_ID}.priv.pem" 2> /dev/null | base64 | head -c 26 | sed 's/\//A/g')
echo "${main_password}${random_digit}${random_upper}${random_lower}${random_special}"
}
# This password only contains alphanumeric characters
generate_simple_password(){
local seed_text="$1"
local combined_text="This is a salt string to generate one consistent password for ${seed_text}. It is not required to be secret."
echo "${combined_text}" | openssl rsautl -sign -inkey "/etc/bridgehead/pki/${SITE_ID}.priv.pem" 2> /dev/null | base64 | head -c 26 | sed 's/[+\/]/A/g'
}

View File

@ -67,29 +67,30 @@ log INFO "Checking network access ($BROKER_URL_FOR_PREREQ) ..."
source /etc/bridgehead/${PROJECT}.conf
source ${PROJECT}/vars
set +e
SERVERTIME="$(https_proxy=$HTTPS_PROXY_FULL_URL curl -m 5 -s -I $BROKER_URL_FOR_PREREQ 2>&1 | grep -i -e '^Date: ' | sed -e 's/^Date: //i')"
RET=$?
set -e
if [ $RET -ne 0 ]; then
log WARN "Unable to connect to Samply.Beam broker at $BROKER_URL_FOR_PREREQ. Please check your proxy settings.\nThe currently configured proxy was \"$HTTPS_PROXY_URL\". This error is normal when using proxy authentication."
log WARN "Unable to check clock skew due to previous error."
else
log INFO "Checking clock skew ..."
if [ "${PROJECT}" != "minimal" ]; then
set +e
SERVERTIME="$(https_proxy=$HTTPS_PROXY_FULL_URL curl -m 5 -s -I $BROKER_URL_FOR_PREREQ 2>&1 | grep -i -e '^Date: ' | sed -e 's/^Date: //i')"
RET=$?
set -e
if [ $RET -ne 0 ]; then
log WARN "Unable to connect to Samply.Beam broker at $BROKER_URL_FOR_PREREQ. Please check your proxy settings.\nThe currently configured proxy was \"$HTTPS_PROXY_URL\". This error is normal when using proxy authentication."
log WARN "Unable to check clock skew due to previous error."
else
log INFO "Checking clock skew ..."
SERVERTIME_AS_TIMESTAMP=$(date --date="$SERVERTIME" +%s)
MYTIME=$(date +%s)
SKEW=$(($SERVERTIME_AS_TIMESTAMP - $MYTIME))
SKEW=$(echo $SKEW | awk -F- '{print $NF}')
SYNCTEXT="For example, consider entering a correct NTP server (e.g. your institution's Active Directory Domain Controller in /etc/systemd/timesyncd.conf (option NTP=) and restart systemd-timesyncd."
if [ $SKEW -ge 300 ]; then
report_error 5 "Your clock is not synchronized (${SKEW}s off). This will cause Samply.Beam's certificate will fail. Please setup time synchronization. $SYNCTEXT"
exit 1
elif [ $SKEW -ge 60 ]; then
log WARN "Your clock is more than a minute off (${SKEW}s). Consider syncing to a time server. $SYNCTEXT"
fi
SERVERTIME_AS_TIMESTAMP=$(date --date="$SERVERTIME" +%s)
MYTIME=$(date +%s)
SKEW=$(($SERVERTIME_AS_TIMESTAMP - $MYTIME))
SKEW=$(echo $SKEW | awk -F- '{print $NF}')
SYNCTEXT="For example, consider entering a correct NTP server (e.g. your institution's Active Directory Domain Controller in /etc/systemd/timesyncd.conf (option NTP=) and restart systemd-timesyncd."
if [ $SKEW -ge 300 ]; then
report_error 5 "Your clock is not synchronized (${SKEW}s off). This will cause Samply.Beam's certificate will fail. Please setup time synchronization. $SYNCTEXT"
exit 1
elif [ $SKEW -ge 60 ]; then
log WARN "Your clock is more than a minute off (${SKEW}s). Consider syncing to a time server. $SYNCTEXT"
fi
fi
fi
checkPrivKey() {
if [ -e /etc/bridgehead/pki/${SITE_ID}.priv.pem ]; then
log INFO "Success - private key found."
@ -100,7 +101,7 @@ checkPrivKey() {
return 0
}
if [[ "$@" =~ "noprivkey" ]]; then
if [[ "$@" =~ "noprivkey" || "${PROJECT}" != "minimal" ]]; then
log INFO "Skipping check for private key for now."
else
checkPrivKey || exit 1

View File

@ -86,7 +86,7 @@ done
# Check docker updates
log "INFO" "Checking for updates to running docker images ..."
docker_updated="false"
for IMAGE in $(cat $PROJECT/docker-compose.yml ${OVERRIDE//-f/} minimal/docker-compose.yml | grep -v "^#" | grep "image:" | sed -e 's_^.*image: \(.*\).*$_\1_g; s_\"__g'); do
for IMAGE in $($COMPOSE -p $PROJECT -f ./minimal/docker-compose.yml -f ./$PROJECT/docker-compose.yml $OVERRIDE config | grep "image:" | sed -e 's_^.*image: \(.*\).*$_\1_g; s_\"__g'); do
log "INFO" "Checking for Updates of Image: $IMAGE"
if docker pull $IMAGE | grep "Downloaded newer image"; then
CHANGE="Image $IMAGE updated."

View File

@ -55,5 +55,6 @@ services:
HOST: ${HOST}
PROJECT: ${PROJECT}
SITE_NAME: ${SITE_NAME}
ENVIRONMENT: "production"

View File

@ -18,7 +18,7 @@ services:
- "forward_proxy"
volumes:
- /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro
- /srv/docker/bridgehead/ccp/root.crt.pem:/conf/root.crt.pem:ro
- /etc/bridgehead/dnpm/aachen.crt.pem:/conf/root.crt.pem:ro
dnpm-beam-connect:
depends_on: [ dnpm-beam-proxy ]
@ -32,12 +32,14 @@ services:
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
NO_PROXY: dnpm-beam-proxy,dnpm-backend, host.docker.internal${DNPM_ADDITIONAL_NO_PROXY}
RUST_LOG: ${RUST_LOG:-info}
NO_AUTH: "true"
TLS_CA_CERTIFICATES_DIR: ./conf/trusted-ca-certs
extra_hosts:
- "host.docker.internal:host-gateway"
volumes:
- /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro
- /etc/bridgehead/dnpm/local_targets.json:/conf/connect_targets.json:ro
- /etc/bridgehead/dnpm/central_targets.json:/conf/central_targets.json:ro
labels:
@ -48,6 +50,10 @@ services:
- "traefik.http.services.dnpm-connect.loadbalancer.server.port=8062"
- "traefik.http.routers.dnpm-connect.tls=true"
dnpm-echo:
image: docker.verbis.dkfz.de/cache/samply/bridgehead-echo:latest
container_name: bridgehead-dnpm-echo
secrets:
proxy.pem:
file: /etc/bridgehead/pki/${SITE_ID}.priv.pem

View File

@ -6,6 +6,7 @@ services:
container_name: bridgehead-dnpm-backend
environment:
- ZPM_SITE=${ZPM_SITE}
- N_RANDOM_FILES=${DNPM_SYNTH_NUM}
volumes:
- /etc/bridgehead/dnpm:/bwhc_config:ro
- ${DNPM_DATA_DIR}:/bwhc_data

View File

@ -14,14 +14,15 @@ if [ -n "${ENABLE_DNPM_NODE}" ]; then
log ERROR "Mandatory variable DNPM_DATA_DIR not defined!"
exit 1
fi
if grep -q 'traefik.http.routers.landing.rule=PathPrefix(`/landing`)' /srv/docker/bridgehead/minimal/docker-compose.override.yml 2>/dev/null; then
echo "Override of landing page url already in place"
else
echo "Adding override of landing page url"
if [ -f /srv/docker/bridgehead/minimal/docker-compose.override.yml ]; then
echo -e ' landing:\n labels:\n - "traefik.http.routers.landing.rule=PathPrefix(`/landing`)"' >> /srv/docker/bridgehead/minimal/docker-compose.override.yml
else
echo -e 'version: "3.7"\nservices:\n landing:\n labels:\n - "traefik.http.routers.landing.rule=PathPrefix(`/landing`)"' >> /srv/docker/bridgehead/minimal/docker-compose.override.yml
fi
fi
DNPM_SYNTH_NUM=${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
fi

View File

@ -6,11 +6,17 @@ if [ -n "${ENABLE_DNPM}" ]; then
# Set variables required for Beam-Connect
DNPM_BEAM_SECRET_SHORT="$(cat /proc/sys/kernel/random/uuid | sed 's/[-]//g' | head -c 20)"
DNPM_BROKER_ID="broker.ccp-it.dktk.dkfz.de"
DNPM_BROKER_ID="dnpm-aachen-broker.samply.de"
DNPM_BROKER_URL="https://${DNPM_BROKER_ID}"
if [ -z ${BROKER_URL_FOR_PREREQ+x} ]; then
BROKER_URL_FOR_PREREQ=$DNPM_BROKER_URL
log DEBUG "No Broker for clock check set; using $DNPM_BROKER_URL"
fi
DNPM_PROXY_ID="${SITE_ID}.${DNPM_BROKER_ID}"
# If the DNPM_NO_PROXY variable is set, prefix it with a comma (as it gets added to a comma separated list)
if [ -n "${DNPM_NO_PROXY}" ]; then
DNPM_ADDITIONAL_NO_PROXY=",${DNPM_NO_PROXY}"
else
DNPM_ADDITIONAL_NO_PROXY=""
fi
fi